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Grain-related Traits in Maize: Genome-wide Association Analysis and Candidate Gene Prediction
CHENXinyi, LIUChenyan, HUAMingzhu, XUXin, FENGWenxiang, WANGBaohua, FANGHui
PDF(2139 KB)
PDF(2139 KB)
Grain-related Traits in Maize: Genome-wide Association Analysis and Candidate Gene Prediction
To explore the natural variations in regulating the maize kernel development and to assist in the genetic improvement of maize yield traits, in this study, 150 maize inbred lines with rich genetic variations were selected as materials for investigation. Combining 34,342 SNP markers and three models, a genome-wide association analysis was conducted on five grain-related traits. The results revealed that a total of 18 independent loci were significantly associated with the target traits, with each locus accounting for 12.24% to 15.41% of the phenotypic variations. Additionally, significant epistatic interactions were identified among four pairs of SNPs associated with kernel length, collectively explaining 5.32% of the phenotypic variations. By integrating the dynamic transcriptome data of kernel development in the B73 inbred line and functional annotations of genes, 19 candidate genes were predicted and classified into four categories: 6 enzymes, 3 ribosomal proteins, 1 transcription factor, and 9 other proteins. These candidate genes provide new genetic resources for deciphering the molecular mechanisms of maize kernel development and enhancing maize kernel size and yield. Through this research, we have not only uncovered the natural variations that regulate the development of corn kernels but also provided new genetic resources for the genetic improvement of corn yield traits. These findings are expected to bring new breakthroughs in corn breeding efforts, enhance corn production, and thereby better meet human needs for food.
maize / kernel size / yield / genome-wide association analysis / candidate genes prediction {{custom_keyword}} /
表1 5个玉米籽粒相关性状的描述性统计及遗传力 |
| 性状 | 自交系个数 | 最小值 | 最大值 | 平均值±标准差 | 变异系数 | 广义遗传力 | 置信区间 |
|---|---|---|---|---|---|---|---|
| HKW/g | 150 | 8.28 | 31.07 | 20.49 ± 4.12 | 20.11 | 0.995 | 0.994~0.997 |
| KL/mm | 150 | 7.37 | 10.00 | 8.75 ± 0.51 | 5.83 | 0.653 | 0.530~0.744 |
| KW/mm | 150 | 6.82 | 9.08 | 8.17 ± 0.37 | 4.53 | 0.916 | 0.886~0.938 |
| KT/mm | 150 | 3.97 | 6.12 | 4.79 ± 0.41 | 8.56 | 0.849 | 0.795~0.888 |
| KV/mL | 150 | 0.10 | 0.26 | 0.17 ± 0.03 | 17.65 | 0.523 | 0.354~0.647 |
表2 5个玉米籽粒性状之间的相关性 |
| HKW | KL | KW | KT | KV | |
|---|---|---|---|---|---|
| HKW | 1 | 4.62E-16 | 5.70E-16 | 3.25E-11 | 3.32E-31 |
| KL | 0.65 | 1 | 3.34E-05 | 2.05E-01 | 4.87E-12 |
| KW | 0.65 | 0.36 | 1 | 3.42E-02 | 1.03E-09 |
| KT | 0.55 | 0.12 | 0.19 | 1 | 2.23E-09 |
| KV | 0.82 | 0.57 | 0.52 | 0.51 | 1 |
| 注：左下部分表示性状之间的相关性；右上部分表示P值。 |
表3 5个玉米籽粒相关性状的全基因组关联分析结果及候选基因预测 |
| 性状 | 标记 | 染色体 | 物理位置 | P值 | R2/% | 候选基因_V3 | 候选基因_V4 | 功能注释 | 备注 | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| KL | PUT-163a-4730462-2143 | 1 | 49131053 | 7.94E-05 | 12.51 | GRMZM2G038015 | Zm00001d028879 | bZIP-transcription factor 24 | ||||||||||
| KL | PZE-101070408 | 1 | 53158367 | 5.13E-05 | 13.56 | GRMZM2G107463 | Zm00001d028989 | RING/U-box superfamily protein | ||||||||||
| HKW | SYN29761 | 1 | 90219767 | 2.75E-05 | 14.29 | GRMZM2G154487 | Zm00001d029887 | Ribosomal L18p/L5e family protein | ||||||||||
| KV | PZE-102077877 | 2 | 60656421 | 5.47E-05 | 13.80 | GRMZM2G016749 | Zm00001d000124 | Protein-serine/threonine phosphatase | ||||||||||
| KW | PZE-103124207 | 3 | 181695567 | 1.10E-05 | 15.41 | GRMZM2G386991 | Zm00001d042938 | Serine/threonine-protein kinase AFC1 | ||||||||||
| KL | ZM013522-0530 | 3 | 222667473 | 1.22E-05 | 15.26 | GRMZM5G866024 | Zm00001d044376 | membrane protein | ||||||||||
| KT | SYNGENTA2236 | 4 | 5010855 | 8.07E-05 | 12.86 | GRMZM2G101502 | Zm00001d018506 | Deoxyhypusine hydroxylase | 条件 分析 | |||||||||
| KL | SYN3700 | 5 | 216163416 | 1.93E-05 | 14.62 | GRMZM2G101571 | Zm00001d018507 | bet1 sft1-related snare | ||||||||||
| KL | PZE-106060527 | 6 | 109295972 | 1.13E-05 | 15.25 | GRMZM2G048194 | Zm00001d037151 | erwinia induced protein 1 | ||||||||||
| KV | PZE-106082684 | 6 | 139912054 | 9.34E-05 | 12.71 | GRMZM2G068496 | Zm00001d037972 | 60S ribosomal protein L29 | 条件分析 | |||||||||
| GRMZM2G068323 | Zm00001d037975 | pentatricopeptide repeat-containing protein | ||||||||||||||||
| HKW | SYN38610 | 6 | 165943896 | 7.25E-05 | 12.74 | GRMZM2G132929 | Zm00001d039106 | 40S ribosomal protein S12-like | ||||||||||
| HKW | PZE-108019862 | 8 | 17889483 | 8.97E-05 | 12.47 | GRMZM2G080722 | Zm00001d008736 | Monothiol glutaredoxin-S4, mitochondrial | ||||||||||
| KT | PZE-108040469 | 8 | 65972918 | 1.05E-05 | 15.35 | GRMZM2G021331 | Zm00001d009488 | ATP synthase beta chain | ||||||||||
| KL | PZE-108113799 | 8 | 164939218 | 7.41E-05 | 14.74 | GRMZM2G049269 | Zm00001d012211 | ankyrin-like protein | ||||||||||
| KL | PZE-109030021 | 9 | 33672066 | 7.05E-05 | 12.78 | GRMZM2G065355 | Zm00001d045724 | heat shock factor-binding protein 1 | ||||||||||
| KL | SYN32340 | 9 | 90842290 | 6.11E-05 | 13.20 | GRMZM2G056166 | Zm00001d046531 | bri1-kd interacting protein 118 | ||||||||||
| KL | PZE-109077339 | 9 | 124770857 | 2.27E-05 | 14.39 | GRMZM2G113866 | Zm00001d047335 | sigma factor sigB regulation protein rsbQ | ||||||||||
| KL | PZE-110109454 | 10 | 148515533 | 9.38E-05 | 12.24 | GRMZM2G173636 | Zm00001d026639 | acyl-binding domain-containing protein 6 | ||||||||||
表4 玉米籽粒相关性状的上位性互作分析结果 |
| 性状 | SNP1 | SNP2 | P值 | add_R2/%a | epi_R2/%b |
|---|---|---|---|---|---|
| KL | PUT-163a-4730462-2143 | ZM013522-0530 | 0.02 | 53.39 | 5.32 |
| KL | PUT-163a-4730462-2143 | PZE-109077339 | 0.03 | 53.39 | 5.32 |
| KL | PZE-101070408 | PZE-110109454 | 0.02 | 53.39 | 5.32 |
| KL | PZE-108113799 | PZE-109077339 | 0.01 | 53.39 | 5.32 |
| KV | - | - | - | 20.13 | - |
| KT | - | - | - | 22.63 | - |
| HKW | - | - | - | 22.79 | - |
| KV | - | - | - | 15.41 | - |
| 注：a表示与性状显著关联的加性位点解释的表型变异；b表示与性状显著关联位点的上位性互作解释的表型变异；“-”表示无上位性互作。 |
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\n Grain starch and protein are synthesized during endosperm development, prompting the question of what regulatory mechanism underlies the synchronization of the accumulation of secondary and primary gene products. We found that two endosperm-specific NAC transcription factors, ZmNAC128 and ZmNAC130, have such a regulatory function. Knockdown of expression of\n ZmNAC128\n and\n ZmNAC130\n with RNA interference (RNAi) caused a shrunken kernel phenotype with significant reduction of starch and protein. We could show that ZmNAC128 and ZmNAC130 regulate the transcription of\n Bt2\n and then reduce its protein level, a rate-limiting step in starch synthesis of maize endosperm. Lack of ZmNAC128 and ZmNAC130 also reduced accumulation of zeins and nonzeins by 18% and 24% compared with nontransgenic siblings, respectively. Although ZmNAC128 and ZmNAC130 affected expression of zein genes in general, they specifically activated transcription of the\n 16-kDa γ-zein\n gene. The two transcription factors did not dimerize with each other but exemplified redundancy, whereas individual discovery of their function was not amenable to conventional genetics but illustrated the power of RNAi. Given that both the\n Bt2\n and the\n 16-kDa γ-zein\n genes were activated by ZmNAC128 or ZmNAC130, we could identify a core binding site ACGCAA contained within their target promoter regions by combining Dual-Luciferase Reporter and Electrophoretic Mobility Shift assays. Consistent with these properties, transcriptomic profiling uncovered that lack of ZmNAC128 and ZmNAC130 had a pleiotropic effect on the utilization of carbohydrates and amino acids.\n
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To explore the function of Dof transcription factors during kernel development in maize, we first identified Dof genes in the maize genome. We found that ZmDof3 was exclusively expressed in the endosperm of maize kernel and had the features of a Dof transcription factor. Suppression of ZmDof3 resulted in a defective kernel phenotype with reduced starch content and a partially patchy aleurone layer. The expression levels of starch synthesis-related genes and aleurone differentiation-associated genes were down-regulated in ZmDof3 knockdown kernels, indicating that ZmDof3 plays an important role in maize endosperm development. The maize endosperm, occupying a large proportion of the kernel, plays an important role in seed development and germination. Current knowledge regarding the regulation of endosperm development is limited. Dof proteins, a family of plant-specific transcription factors, play critical roles in diverse biological processes. In this study, an endosperm-specific Dof protein gene, ZmDof3, was identified in maize through genome-wide screening. Suppression of ZmDof3 resulted in a defective kernel phenotype. The endosperm of ZmDof3 knockdown kernels was loosely packed with irregular starch granules observed by electronic microscope. Through genome-wide expression profiling, we found that down-regulated genes were enriched in GO terms related to carbohydrate metabolism. Moreover, ZmDof3 could bind to the Dof core element in the promoter of starch biosynthesis genes Du1 and Su2 in vitro and in vivo. In addition, the aleurone at local position in mature ZmDof3 knockdown kernels varied from one to three layers, which consisted of smaller and irregular cells. Further analyses showed that knockdown of ZmDof3 reduced the expression of Nkd1, which is involved in aleurone cell differentiation, and that ZmDof3 could bind to the Dof core element in the Nkd1 promoter. Our study reveals that ZmDof3 functions in maize endosperm development as a positive regulator in the signaling system controlling starch accumulation and aleurone development.
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The miniature1 (mn1) seed phenotype is a loss-of-function mutation at the Mn1 locus that encodes a cell wall invertase; its deficiency leads to pleiotropic changes including altered sugar levels and decreased levels of IAA throughout seed development. To understand the molecular details of such a sugar-hormone relationship, we have initiated studies on IAA biosynthesis genes in developing seeds of maize. Two tryptophan-dependent pathways of IAA biosynthesis, tryptamine (TAM) and indole-3-pyruvic acid (IPA), are of particular interest. We report on molecular isolation and characterization of an endosperm-specific ZmTARelated1 (ZmTar1) gene of the IPA branch; we have also reported recently on ZmYuc1 gene in the TAM branch. Comparative gene expression analyses here have shown that (1) the ZmTar1 transcripts were approximately 10-fold higher levels than the ZmYuc1; (2) although both genes showed the highest level of expression at 8-12 d after pollination (DAP) coincident with an early peak in IAA levels, the two showed highly divergent (antagonistic) response at 12 and 16 DAP but similar patterns at 20 and 28 DAP in the Mn1 and mn1 endosperm. The Western blot analyses for the ZmTAR1 protein, however, displayed disconcordant protein/transcript expression patterns. Overall, these data report novel observations on redundant trp-dependent pathways of auxin biosynthesis in developing seeds of maize, and suggest that homeostatic control of IAA in this important sink is highly complex and may be regulated by both sucrose metabolism and developmental signals.
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To study the influence of PINFORMED1 (PIN1)-mediated auxin transport during embryogenesis and endosperm development in monocots, the expression pattern of the three identified ZmPIN1 genes was determined at the transcript level. Localization of the corresponding proteins was also analyzed during maize (Zea mays) kernel development. An anti-indole-3-acetic acid (IAA) monoclonal antibody was used to visualize IAA distribution and correlate the direction of auxin active transport, mediated by ZmPIN1 proteins, with the actual amount of auxin present in maize kernels at different developmental stages. ZmPIN1 genes are expressed in the endosperm soon after double fertilization occurs; however, unlike other tissues, the ZmPIN1 proteins were never polarly localized in the plasma membrane of endosperm cells. ZmPIN1 transcripts and proteins also colocalize in developing embryos, and the ZmPIN1 proteins are polarly localized in the embryo cell plasma membrane from the first developmental stages, indicating the existence of ZmPIN1-mediated auxin fluxes. Auxin distribution visualization indicates that the aleurone, the basal endosperm transfer layer, and the embryo-surrounding region accumulate free auxin, which also has a maximum in the kernel maternal chalaza. During embryogenesis, polar auxin transport always correlates with the differentiation of embryo tissues and the definition of the embryo organs. On the basis of these reports and of the observations on tissue differentiation and IAA distribution in defective endosperm-B18 mutant and in N-1-naphthylphthalamic acid-treated kernels, a model for ZmPIN1-mediated transport of auxin and the related auxin fluxes during maize kernel development is proposed. Common features between this model and the model previously proposed for Arabidopsis (Arabidopsis thaliana) are discussed.
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In flowering plants, many respiration-related proteins are encoded by the mitochondrial genome and the splicing of mitochondrion-encoded messenger RNA (mRNA) involves a complex collaboration with nuclear-encoded proteins. Pentatricopeptide repeat (PPR) proteins have been implicated in these RNA-protein interactions. Maize defective kernel 2 (dek2) is a classic mutant with small kernels and delayed development. Through positional cloning and allelic confirmation, we found Dek2 encodes a novel P-type PPR protein that targets mitochondria. Mitochondrial transcript analysis indicated that dek2 mutation causes reduced splicing efficiency of mitochondrial nad1 intron 1. Mitochondrial complex analysis in dek2 immature kernels showed severe deficiency of complex I assembly. Dramatically up-regulated expression of alternative oxidases (AOXs), transcriptome data, and TEM analysis results revealed that proper splicing of nad1 is critical for mitochondrial functions and inner cristaes morphology. This study indicated that Dek2 is a new PPR protein that affects the splicing of mitochondrial nad1 intron 1 and is required for mitochondrial function and kernel development.Copyright © 2017 by the Genetics Society of America.
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Respiration, the core of mitochondrial metabolism, depends on the function of five respiratory complexes. Many respiratory chain-related proteins are encoded by the mitochondrial genome and their RNAs undergo post-transcriptional modifications by nuclear genome-expressed factors, including pentatricopeptide repeat (PPR) proteins. Maize defective kernel 10 (dek10) is a classic mutant with small kernels and delayed development. Through positional cloning, we found that Dek10 encodes an E-subgroup PPR protein localized in mitochondria. Sequencing analysis indicated that Dek10 is responsible for the C-to-U editing at nad3-61, nad3-62, and cox2-550 sites, which are specific editing sites in monocots. The defects of these editing sites result in significant reduction of Nad3 and the loss of Cox2. Interestingly, the assembly of complex I was not reduced, but its NADH dehydrogenase activity was greatly decreased. The assembly of complex IV was significantly reduced. Transcriptome and transmission electron microscopy (TEM) analysis revealed that proper editing of nad3 and cox2 is critical for mitochondrial functions, biogenesis, and morphology. These results indicate that the E-subgroup PPR protein Dek10 is responsible for multiple editing sites in nad3 and cox2, which are essential for mitochondrial functions and plant development in maize.
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The organic acid oxalate occurs in microbes, animals, and plants; however, excessive oxalate accumulation in vivo is toxic to cell growth and decreases the nutritional quality of certain vegetables. However, the enzymes and functions required for oxalate degradation in plants remain largely unknown. Here, we report the cloning of a maize () opaque endosperm mutant that encodes oxalyl-CoA decarboxylase1 (EC4.1.1.8; OCD1). is generally expressed and is specifically induced by oxalate. The mutant seeds contain a significantly higher level of oxalate than the wild type, indicating that the mutants have a defect in oxalate catabolism. The maize classic mutant () was initially cloned for its high lysine trait, although the gene function was not understood until its homolog in was found to encode an oxalyl-CoA synthetase (EC 6.2.1.8), which ligates oxalate and CoA to form oxalyl-CoA. Our enzymatic analysis showed that ZmOCD1 catalyzes oxalyl-CoA, the product of O7, into formyl-CoA and CO for degradation. Mutations in caused dramatic alterations in the metabolome in the endosperm. Our findings demonstrate that ZmOCD1 acts downstream of O7 in oxalate degradation and affects endosperm development, the metabolome, and nutritional quality in maize seeds.© 2018 American Society of Plant Biologists. All rights reserved.
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龚玉林, 贺丹, 卫芸芸, 等. 真菌遗传学方法研究进展[J]. 菌物研究, 2019, 17(3):173-179.
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Maize is one of the most important crops globally, and it shows remarkable genetic diversity. Knowledge of this diversity could help in crop improvement; however, gold-standard genomes have been elucidated only for modern temperate varieties. Here, we present a high-quality reference genome (contig N50 of 15.78 megabases) of the maize small-kernel inbred line, which is derived from a tropical landrace. Using haplotype maps derived from B73, Mo17 and SK, we identified 80,614 polymorphic structural variants across 521 diverse lines. Approximately 22% of these variants could not be detected by traditional single-nucleotide-polymorphism-based approaches, and some of them could affect gene expression and trait performance. To illustrate the utility of the diverse SK line, we used it to perform map-based cloning of a major effect quantitative trait locus controlling kernel weight-a key trait selected during maize improvement. The underlying candidate gene ZmBARELY ANY MERISTEM1d provides a target for increasing crop yields.
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Huangzaosi, Qi319, and Ye478 are foundation inbred lines widely used in maize breeding in China. To elucidate genetic base of yield components and kernel-related traits in these elite lines, two F(2:3) populations derived from crosses Qi319 × Huangzaosi (Q/H, 230 families) and Ye478 × Huangzaosi (Y/H, 235 families), as well as their parents were evaluated in six environments including Henan, Beijing, and Xinjiang in 2007 and 2008. Correlation and hypergeometric probability function analyses showed the dependence of yield components on kernel-related traits. Three mapping procedures were used to identify quantitative trait loci (QTL) for each population: (1) analysis for each of the six environments, (2) joint analysis for each of the three locations across 2 years, and (3) joint analysis across all environments. For the eight traits measured, 90, 89, and 58 QTL for Q/H, and 72, 76, and 51 QTL for Y/H were detected by the three QTL mapping procedures, respectively. About 70% of the QTL from Q/H and 90% of the QTL from Y/H did not show significant QTL × environment interactions in the joint analysis across all environments. Most of the QTL for kernel traits exhibited high stability across 2 years at the same location, even across different locations. Seven major QTL detected under at least four environments were identified on chromosomes 1, 4, 6, 7, 9, and 10 in the populations. Moreover, QTL on chr. 1, chr. 4, and chr. 9 were detected in both populations. These chromosomal regions could be targets for marker-assisted selection, fine mapping, and map-based cloning in maize.
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The genetic control of yield and related traits in maize has been addressed by many quantitative trait locus (QTL) studies, which have produced a wealth of QTL information, also known as QTLome. In this study, we assembled a yield QTLome database and carried out QTL meta-analysis based on 44 published studies, representing 32 independent mapping populations and 49 parental lines. A total of 808 unique QTLs were condensed to 84 meta-QTLs and were projected on the 10 maize chromosomes. Seventy-four percent of QTLs showed a proportion of phenotypic variance explained (PVE) smaller than 10% confirming the high genetic complexity of grain yield. Yield QTLome projection on the genetic map suggested pericentromeric enrichment of QTLs. Conversely, pericentromeric depletion of QTLs was observed when the physical map was considered, suggesting gene density as the main driver of yield QTL distribution on chromosomes. Dominant and overdominant yield QTLs did not distribute differently from additive effect QTLs.Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.
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Maize () is a major staple crop. Maize kernel size and weight are important contributors to its yield. Here, we measured kernel length, kernel width, kernel thickness, hundred kernel weight, and kernel test weight in 10 recombinant inbred line populations and dissected their genetic architecture using three statistical models. In total, 729 quantitative trait loci (QTLs) were identified, many of which were identified in all three models, including 22 major QTLs that each can explain more than 10% of phenotypic variation. To provide candidate genes for these QTLs, we identified 30 maize genes that are orthologs of 18 rice () genes reported to affect rice seed size or weight. Interestingly, 24 of these 30 genes are located in the identified QTLs or within 1 Mb of the significant single-nucleotide polymorphisms. We further confirmed the effects of five genes on maize kernel size/weight in an independent association mapping panel with 540 lines by candidate gene association analysis. Lastly, the function of, a homolog of rice that affects seed size and weight, was characterized in detail. is close to QTL peaks for kernel size/weight (less than 1 Mb) and contains significant single-nucleotide polymorphisms affecting kernel size/weight in the association panel. Overexpression of this gene can rescue the reduced weight of the Arabidopsis () homozygous mutant line in the gene (Arabidopsis ortholog of ). These results indicate that the molecular mechanisms affecting seed development are conserved in maize, rice, and possibly Arabidopsis.© 2017 American Society of Plant Biologists. All Rights Reserved.
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Maize grain yield and related traits are complex and are controlled by a large number of genes of small effect or quantitative trait loci (QTL). Over the years, a large number of yield-related QTLs have been identified in maize and deposited in public databases. However, integrating and re-analyzing these data and mining candidate loci for yield-related traits has become a major issue in maize. In this study, we collected information on QTLs conferring maize yield-related traits from 33 published studies. Then, 999 of these QTLs were iteratively projected and subjected to meta-analysis to obtain metaQTLs (MQTLs). A total of 76 MQTLs were found across the maize genome. Based on a comparative genomics strategy, several maize orthologs of rice yield-related genes were identified in these MQTL regions. Furthermore, three potential candidate genes (Gene ID: GRMZM2G359974, GRMZM2G301884, and GRMZM2G083894) associated with kernel size and weight within three MQTL regions were identified using regional association mapping, based on the results of the meta-analysis. This strategy, combining MQTL analysis and regional association mapping, is helpful for functional marker development and rapid identification of candidate genes or loci.
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With increasing demand for novel traits in crop breeding, the plant research community faces the challenge of quantitatively analyzing the structure and function of large numbers of plants. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In this study, we quantified 106 traits from a maize () recombinant inbred line population ( = 167) across 16 developmental stages using the automatic phenotyping platform. Quantitative trait locus (QTL) mapping with a high-density genetic linkage map, including 2,496 recombinant bins, was used to uncover the genetic basis of these complex agronomic traits, and 988 QTLs have been identified for all investigated traits, including three QTL hotspots. Biomass accumulation and final yield were predicted using a combination of dissected traits in the early growth stage. These results reveal the dynamic genetic architecture of maize plant growth and enhance ideotype-based maize breeding and prediction.© 2017 American Society of Plant Biologists. All Rights Reserved.
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Starch is the most abundant storage carbohydrate in maize kernels and provides calories for humans and other animals as well as raw materials for various industrial applications. Decoding of the genetic basis of natural variation in kernel starch content is needed to manipulate starch quantity and quality via molecular breeding to meet future needs. Here, we identified 50 unique single quantitative trait loci (QTLs) for starch content with 18 novel QTLs via single linkage mapping, joint linkage mapping, and a genome-wide association study in a multi-parent population containing six recombinant inbred line populations. Only five QTLs explained over 10% of phenotypic variation in single populations. In addition to a few large-effect and many small-effect additive QTLs, limited pairs of epistatic QTLs also contributed to the genetic basis of the variation in kernel starch content. A regional association study identified five non-starch-pathway genes that were the causal candidate genes underlying the identified QTLs for starch content. The pathway-driven analysis identified ZmTPS9, which encodes a trehalose-6-phosphate synthase in the trehalose pathway, as the causal gene for the QTL qSTA4-2, which was detected by all three statistical analyses. Knockout of ZmTPS9 increased kernel starch content and, in turn, kernel weight in maize, suggesting potential applications for ZmTPS9 in maize starch and yield improvement. These findings extend our knowledge about the genetic basis of starch content in maize kernels and provide valuable information for maize genetic improvement of starch quantity and quality.This article is protected by copyright. All rights reserved.
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\n A better understanding of the extent of convergent selection among crops could greatly improve breeding programs. We found that the quantitative trait locus\n KRN2\n in maize and its rice ortholog,\n OsKRN2\n, experienced convergent selection. These orthologs encode WD40 proteins and interact with a gene of unknown function, DUF1644, to negatively regulate grain number in both crops. Knockout of\n KRN2\n in maize or\n OsKRN2\n in rice increased grain yield by ~10% and ~8%, respectively, with no apparent trade-offs in other agronomic traits. Furthermore, genome-wide scans identified 490 pairs of orthologous genes that underwent convergent selection during maize and rice evolution, and these were enriched for two shared molecular pathways.\n KRN2\n, together with other convergently selected genes, provides an excellent target for future crop improvement.\n
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Maize is an important crop species of high genetic diversity. We identified and genotyped several million sequence polymorphisms among 27 diverse maize inbred lines and discovered that the genome was characterized by highly divergent haplotypes and showed 10- to 30-fold variation in recombination rates. Most chromosomes have pericentromeric regions with highly suppressed recombination that appear to have influenced the effectiveness of selection during maize inbred development and may be a major component of heterosis. We found hundreds of selective sweeps and highly differentiated regions that probably contain loci that are key to geographic adaptation. This survey of genetic diversity provides a foundation for uniting breeding efforts across the world and for dissecting complex traits through genome-wide association studies.
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| [35] |
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| [36] |
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| [37] |
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| [38] |
Starch is the most abundant storage carbohydrate in maize kernel. The content of amylose and amylopectin confers unique properties in food processing and industrial application. Thus, the resurgent interest has been switched to the study of individual amylose or amylopectin rather than total starch, whereas the enzymatic machinery for amylose synthesis remains elusive. We took advantage of the phenotype of amylose content and the genotype of 9,007,194 single nucleotide polymorphisms from 464 inbred maize lines. The genome-wide association study identified 27 associated loci involving 39 candidate genes that were linked to amylose content including transcription factors, glycosyltransferases, glycosidases, as well as hydrolases. Except the waxy gene that encodes the granule-bound starch synthase, the remaining candidate genes were located in the upstream pathway of amylose synthesis, while the downstream members were already known from prior studies. The linked candidate genes could be transferred to manipulate amylose content and thus add value to maize kernel in the breeding programme.© 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
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| [39] |
Kernel size-related traits are the most direct traits correlating with grain yield. The genetic basis of three kernel traits of maize, kernel length (KL), kernel width (KW) and kernel thickness (KT), was investigated in an association panel and a biparental population. A total of 21 single nucleotide polymorphisms (SNPs) were detected to be most significantly (P < 2.25 × 10 ) associated with these three traits in the association panel under four environments. Furthermore, 50 quantitative trait loci (QTL) controlling these traits were detected in seven environments in the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, of which eight were repetitively identified in at least three environments. Combining the two mapping populations revealed that 56 SNPs (P < 1 × 10 ) fell within 18 of the QTL confidence intervals. According to the top significant SNPs, stable-effect SNPs and the co-localized SNPs by association analysis and linkage mapping, a total of 73 candidate genes were identified, regulating seed development. Additionally, seven miRNAs were found to situate within the linkage disequilibrium (LD) regions of the co-localized SNPs, of which zma-miR164e was demonstrated to cleave the mRNAs of Arabidopsis CUC1, CUC2 and NAC6 in vitro. Overexpression of zma-miR164e resulted in the down-regulation of these genes above and the failure of seed formation in Arabidopsis pods, with the increased branch number. These findings provide insights into the mechanism of seed development and the improvement of molecular marker-assisted selection (MAS) for high-yield breeding in maize.© 2019 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
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| [40] |
Kernel weight in a unit volume is referred to as kernel test weight (KTW) that directly reflects maize (Zea mays L.) grain quality. In this study, an inter-mated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population and an association panel were used to identify loci responsible for KTW of maize across multiple environments. A total of 18 significant KTW-related single-nucleotide polymorphisms (SNPs) were identified using genome-wide association study (GWAS); they were closely linked to 12 candidate genes. In the IBM Syn10 DH population, linkage analysis detected 19 common quantitative trait loci (QTL), five of which were repeatedly detected among multiple environments. Several verified genes that regulate maize seed development were found in the confidence intervals of the mapped QTL and the LD regions of GWAS, such as ZmYUC1, BAP2, ZmTCRR-1, dek36 and ZmSWEET4c. Combined QTL mapping and GWAS identified one significant SNP that was co-identified in the both populations. Based on the co-localized SNP across the both populations, 17 candidate genes were identified. Of them, Zm00001d044075, Zm00001d044086, and Zm00001d044081 were further identified by candidate gene association study for KTW. Zm00001d044081 encodes homeobox-leucine zipper protein ATHB-4, which has been demonstrated to control apical embryo development in Arabidopsis. Our findings provided insights into the mechanism underlying maize KTW and contributed to the application of molecular-assisted selection of high KTW breeding in maize.
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| [41] |
Using combined linkage and association mapping, 26 stable QTL and six stable SNPs were detected across multiple environments for eight ear and grain morphological traits in maize. One QTL, PKS2, might play an important role in maize yield improvement. In the present study, one bi-parental population and an association panel were used to identify quantitative trait loci (QTL) for eight ear and grain morphological traits. A total of 108 QTL related to these traits were detected across four environments using an ultra-high density bin map constructed using recombinant inbred lines (RILs) derived from a cross between Ye478 and Qi319, and 26 QTL were identified in more than two environments. Furthermore, 64 single nucleotide polymorphisms (SNPs) were found to be significantly associated with the eight ear and grain morphological traits (-log(P) > 4) in an association panel of 240 maize inbred lines. Combining the two mapping populations, a total of 17 pleiotropic QTL/SNPs (pQTL/SNPs) were associated with various traits across multiple environments. PKS2, a stable locus influencing kernel shape identified on chromosome 2 in a genome-wide association study (GWAS), was within the QTL confidence interval defined by the RILs. The candidate region harbored a short 13-Kb LD block encompassing four SNPs (SYN11386, PHM14783.16, SYN11392, and SYN11378). In the association panel, 13 lines derived from the hybrid PI78599 possessed the same allele as Qi319 at the PHM14783.16 (GG) locus, with an average value of 0.21 for KS, significantly lower than that of the 34 lines derived from Ye478 that carried a different allele (0.25, P < 0.05). Therefore, further fine mapping of PKS2 will provide valuable information for understanding the genetic components of grain yield and improving molecular marker-assisted selection (MAS) in maize.
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| [42] |
代力强, 吴律, 董青松, 等. 玉米籽粒长度的全基因组关联分析[J]. 西北农林科技大学学报(自然科学版), 2018, 6.
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渠建洲, 冯文豪, 张兴华, 等. 基于全基因组关联分析解析玉米籽粒大小的遗传结构[J]. 作物学报, 2022, 48(2):304-319.
玉米籽粒大小是产量重要构成因子之一, 也是受多基因调控的复杂数量性状, 挖掘玉米籽粒大小相关性状的关键调控基因, 将有助于提高玉米的产量。本研究以212份优良玉米自交系为材料, 于2018年和2019年分别对粒长、粒宽和粒厚进行测定, 并结合均匀分布于玉米基因组的73,006个单核苷酸多态性(single nucleotide polymorphism, SNP)标记进行全基因组关联分析。基于FarmCPU算法, 在玉米的10条染色体上检测到47个与籽粒大小相关性状关联的SNP。结合B73玉米自交系籽粒发育的动态时空转录数据, 在显著SNP标记的连锁不平衡区域内, 共检测到58个与籽粒大小相关的候选基因, 其编码的蛋白与多种蛋白存在互作关系, 参与并调控多个与籽粒发育密切相关的生物学过程。本研究为解析玉米籽粒发育的分子调控机制, 改良籽粒大小和提高作物产量提供了新的参考。
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| [44] |
肖颖妮, 李高科, 李坤, 等. 甜玉米籽粒体积和粒重的全基因组关联分析[J]. 中国农业大学学报, 2022, 27(7):12-25.
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| [45] |
Galls or the neoplastic growth on plants result from a complex type of interaction between the inducers (Acari, Insects, Microbes and Nematodes) and plants. The present study sheds light on the gall inducing habit of a highly host specific eriophyid mite,Aceria pongamiae,on the leaves ofPongamia pinnataleading to the production of abnormal pouch like outgrowths on the adaxial and abaxial surfaces of the foliage. Each leaf gall is a highly complex, irregular massive structure, and the formation of which often leads to complete destruction of leaves, especially during heavy mite infestation, and thereby adversely affecting the physiology and growth of the host plant.
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| [46] |
Heritability (H) on a progeny mean basis is frequently estimated in recurrent selection experiments for the purpose of estimating the expected progress from family selection; however, appropriate measures of precision have been developed for only a few heritability estimators. The objective of this research was to develop a measure of precision for H for certain balanced linear models. Exact confidence intervals for H were derived and are not restricted to a specific experimental design. The confidence intervals were applied to sorghum [Sorghum bicolor (L.) Moench] half‐sib family data.
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| [47] |
The nutritional traits of maize kernels are important for human and animal nutrition, and these traits have undergone selection to meet the diverse nutritional needs of humans. However, our knowledge of the genetic basis of selecting for kernel nutritional traits is limited. Here, we identified both single and epistatic quantitative trait loci (QTLs) that contributed to the differences of oil and carotenoid traits between maize and teosinte. Over half of teosinte alleles of single QTLs increased the values of the detected oil and carotenoid traits. Based on the pleiotropism or linkage information of the identified single QTLs, we constructed a trait-locus network to help clarify the genetic basis of correlations among oil and carotenoid traits. Furthermore, the selection features and evolutionary trajectories of the genes or loci underlying variations in oil and carotenoid traits revealed that these nutritional traits produced diverse selection events during maize domestication and improvement. To illustrate more, a mutator distance-relative transposable element (TE) in intron 1 of DXS2, which encoded a rate-limiting enzyme in the methylerythritol phosphate pathway, was identified to increase carotenoid biosynthesis by enhancing DXS2 expression. This TE occurs in the grass teosinte, and has been found to have undergone selection during maize domestication and improvement, and is almost fixed in yellow maize. Our findings not only provide important insights into evolutionary changes in nutritional traits, but also highlight the feasibility of reintroducing back into commercial agricultural germplasm those nutritionally important genes hidden in wild relatives.© 2019 The Authors The Plant Journal © 2019 John Wiley & Sons Ltd.
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| [48] |
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单婷玉, 施雯, 王翌婷, 等. 玉米盐胁迫相关性状全基因组关联分析及候选基因预测[J]. 遗传, 2021, 43(12):1159-1169.
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| [51] |
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Association analyses that exploit the natural diversity of a genome to map at very high resolutions are becoming increasingly important. In most studies, however, researchers must contend with the confounding effects of both population and family structure. TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) implements general linear model and mixed linear model approaches for controlling population and family structure. For result interpretation, the program allows for linkage disequilibrium statistics to be calculated and visualized graphically. Database browsing and data importation is facilitated by integrated middleware. Other features include analyzing insertions/deletions, calculating diversity statistics, integration of phenotypic and genotypic data, imputing missing data and calculating principal components.
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| [53] |
As population structure can result in spurious associations, it has constrained the use of association studies in human and plant genetics. Association mapping, however, holds great promise if true signals of functional association can be separated from the vast number of false signals generated by population structure. We have developed a unified mixed-model approach to account for multiple levels of relatedness simultaneously as detected by random genetic markers. We applied this new approach to two samples: a family-based sample of 14 human families, for quantitative gene expression dissection, and a sample of 277 diverse maize inbred lines with complex familial relationships and population structure, for quantitative trait dissection. Our method demonstrates improved control of both type I and type II error rates over other methods. As this new method crosses the boundary between family-based and structured association samples, it provides a powerful complement to currently available methods for association mapping.
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| [54] |
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| [55] |
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| [56] |
Maize (Zea mays) is an excellent cereal model for research on seed development because of its relatively large size for both embryo and endosperm. Despite the importance of seed in agriculture, the genome-wide transcriptome pattern throughout seed development has not been well characterized. Using high-throughput RNA sequencing, we developed a spatiotemporal transcriptome atlas of B73 maize seed development based on 53 samples from fertilization to maturity for embryo, endosperm, and whole seed tissues. A total of 26,105 genes were found to be involved in programming seed development, including 1,614 transcription factors. Global comparisons of gene expression highlighted the fundamental transcriptomic reprogramming and the phases of development. Coexpression analysis provided further insight into the dynamic reprogramming of the transcriptome by revealing functional transitions during maturation. Combined with the published nonseed high-throughput RNA sequencing data, we identified 91 transcription factors and 1,167 other seed-specific genes, which should help elucidate key mechanisms and regulatory networks that underlie seed development. In addition, correlation of gene expression with the pattern of DNA methylation revealed that hypomethylation of the gene body region should be an important factor for the expressional activation of seed-specific genes, especially for extremely highly expressed genes such as zeins. This study provides a valuable resource for understanding the genetic control of seed development of monocotyledon plants. © 2014 American Society of Plant Biologists. All Rights Reserved.
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| [57] |
A naturally occurring unusual amino acid, hypusine [N (epsilon)-(4-amino-2-hydroxybutyl)-lysine] is a component of a single cellular protein, eukaryotic translation initiation factor 5A (eIF5A). It is a modified lysine with structural contribution from the polyamine spermidine. Hypusine is formed in a novel posttranslational modification that involves two enzymes, deoxyhypusine synthase (DHS) and deoxyhypusine hydroxylase (DOHH). eIF5A and deoxyhypusine/hypusine modification are essential for growth of eukaryotic cells. The hypusine synthetic pathway has evolved in eukaryotes and eIF5A, DHS and DOHH are highly conserved, suggesting maintenance of a fundamental cellular function of eIF5A through evolution. The unique feature of the hypusine modification is the strict specificity of the enzymes toward its substrate protein, eIF5A. Moreover, DHS exhibits a narrow specificity toward spermidine. In view of the extraordinary specificity and the requirement for hypusine-containing eIF5A for mammalian cell proliferation, eIF5A and the hypusine biosynthetic enzymes present new potential targets for intervention in aberrant cell proliferation.
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| [58] |
Genome-wide association study (GWAS) has become a widely accepted strategy for decoding genotype-phenotype associations in many species thanks to advances in next-generation sequencing (NGS) technologies. Maize is an ideal crop for GWAS and significant progress has been made in the last decade. This review summarizes current GWAS efforts in maize functional genomics research and discusses future prospects in the omics era. The general goal of GWAS is to link genotypic variations to corresponding differences in phenotype using the most appropriate statistical model in a given population. The current review also presents perspectives for optimizing GWAS design and analysis. GWAS analysis of data from RNA, protein, and metabolite-based omics studies is discussed, along with new models and new population designs that will identify causes of phenotypic variation that have been hidden to date. The joint and continuous efforts of the whole community will enhance our understanding of maize quantitative traits and boost crop molecular breeding designs.Copyright © 2016 The Author. Published by Elsevier Inc. All rights reserved.
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| [59] |
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| [60] |
Drought represents a major constraint on maize production worldwide. Understanding the genetic basis for natural variation in drought tolerance of maize may facilitate efforts to improve this trait in cultivated germplasm. Here, using a genome-wide association study, we show that a miniature inverted-repeat transposable element (MITE) inserted in the promoter of a NAC gene (ZmNAC111) is significantly associated with natural variation in maize drought tolerance. The 82-bp MITE represses ZmNAC111 expression via RNA-directed DNA methylation and H3K9 dimethylation when heterologously expressed in Arabidopsis. Increasing ZmNAC111 expression in transgenic maize enhances drought tolerance at the seedling stage, improves water-use efficiency and induces upregulation of drought-responsive genes under water stress. The MITE insertion in the ZmNAC111 promoter appears to have occurred after maize domestication and spread among temperate germplasm. The identification of this MITE insertion provides insight into the genetic basis for natural variation in maize drought tolerance.
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| [61] |
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| [63] |
Salt stress is a major devastating abiotic factor that affects the yield and quality of maize. However, knowledge of the molecular mechanisms of the responses to salt stress in maize is limited. To elucidate the genetic basis of salt tolerance traits, a genome-wide association study was performed on 348 maize inbred lines under normal and salt stress conditions using 557 894 single nucleotide polymorphisms (SNPs). The phenotypic data for 27 traits revealed coefficients of variation of >25%. In total, 149 significant SNPs explaining 6.6%-11.2% of the phenotypic variation for each SNP were identified. Of the 104 identified quantitative trait loci (QTLs), 83 were related to salt tolerance and 21 to normal traits. Additionally, 13 QTLs were associated with two to five traits. Eleven and six QTLs controlling salt tolerance traits and normal root growth, respectively, co-localized with QTL intervals reported previously. Based on functional annotations, 13 candidate genes were predicted. Expression levels analysis of 12 candidate genes revealed that they were all responsive to salt stress. The CRISPR/Cas9 technology targeting three sites was applied in maize, and its editing efficiency reached 70%. By comparing the biomass of three CRISPR/Cas9 mutants of ZmCLCg and one zmpmp3 EMS mutant with their wild-type plants under salt stress, the salt tolerance function of candidate genes ZmCLCg and ZmPMP3 were confirmed. Chloride content analysis revealed that ZmCLCg regulated chloride transport under sodium chloride stress. These results help to explain genetic variations in salt tolerance and provide novel loci for generating salt-tolerant maize lines.© 2021 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
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| [64] |
Sodium (Na+) toxicity is one of the major damages imposed on crops by saline-alkaline stress. Here we show that natural maize inbred lines display substantial variations in shoot Na+ contents and saline-alkaline (NaHCO3) tolerance, and reveal that ZmNSA1 (Na+Content under Saline-Alkaline Condition) confers shoot Na+ variations under NaHCO3 condition by a genome-wide association study. Lacking of ZmNSA1 promotes shoot Na+ homeostasis by increasing root Na+ efflux. A naturally occurred 4-bp deletion decreases the translation efficiency of ZmNSA1 mRNA, thus promotes Na+ homeostasis. We further show that, under saline-alkaline condition, Ca2+ binds to the EF-hand domain of ZmNSA1 then triggers its degradation via 26S proteasome, which in turn increases the transcripts levels of PM-H+-ATPases (MHA2 and MHA4), and consequently enhances SOS1 Na+/H+ antiporter-mediated root Na+ efflux. Our studies reveal the mechanism of Ca2+-triggered saline-alkaline tolerance and provide an important gene target for breeding saline-alkaline tolerant maize varieties.
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| [65] |
Maize (Zea mays L.) is a cold-sensitive species that often faces chilling stress, which adversely affects growth and reproduction. However, the genetic basis of low-temperature adaptation in maize remains unclear. Here, we demonstrate that natural variation in the type-A Response Regulator 1 (ZmRR1) gene leads to differences in chilling tolerance among maize inbred lines. Association analysis reveals that InDel-35 of ZmRR1, encoding a protein harboring a mitogen-activated protein kinase (MPK) phosphorylation residue, is strongly associated with chilling tolerance. ZmMPK8, a negative regulator of chilling tolerance, interacts with and phosphorylates ZmRR1 at Ser15. The deletion of a 45-bp region of ZmRR1 harboring Ser15 inhibits its degradation via the 26 S proteasome pathway by preventing its phosphorylation by ZmMPK8. Transcriptome analysis indicates that ZmRR1 positively regulates the expression of ZmDREB1 and Cellulose synthase (CesA) genes to enhance chilling tolerance. Our findings thus provide a potential genetic resource for improving chilling tolerance in maize.© 2021. The Author(s).
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| [66] |
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| [67] |
\n Maize was domesticated from teosinte in Southern Mexico roughly 9,000 years ago. Maize originally was sensitive to photoperiod and required short-day conditions to flower. Thus, the reduced sensitivity to photoperiod is prerequisite for maize spread to long-day temperate regions. A gene encoding a CCT domain-containing protein,\n ZmCCT\n, was found by many researchers to modulate photoperiod sensitivity. The current study shows that insertion of a CACTA-like transposon into the\n ZmCCT\n promoter can suppress the\n ZmCCT\n expression remarkably and thus attenuates maize sensitivity under long-day conditions. The transposable element (TE) insertion event occurred in a tropical maize plant and has been selected for and accumulated as maize adapted to vast long-day environments. This selection leaves behind a TE-related linkage disequilibrium block with the very-low-nucleotide variations.\n
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| [68] |
丁安明, 屈旭, 李凌, 等. 植物PPR蛋白家族研究进展[J]. 中国农学通报, 2014, 30(9):218-224.
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Pentatricopeptide repeat (PPR) proteins constitute one of the largest protein families in land plants, with more than 400 members in most species. Over the past decade, much has been learned about the molecular functions of these proteins, where they act in the cell, and what physiological roles they play during plant growth and development. A typical PPR protein is targeted to mitochondria or chloroplasts, binds one or several organellar transcripts, and influences their expression by altering RNA sequence, turnover, processing, or translation. Their combined action has profound effects on organelle biogenesis and function and, consequently, on photosynthesis, respiration, plant development, and environmental responses. Recent breakthroughs in understanding how PPR proteins recognize RNA sequences through modular base-specific contacts will help match proteins to potential binding sites and provide a pathway toward designing synthetic RNA-binding proteins aimed at desired targets.
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| [70] |
In flowering plants, RNA editing is a posttranscriptional mechanism that converts specific cytidines to uridines in both mitochondrial and plastidial transcripts, altering the information encoded by these genes. Here, we report the molecular characterization of the empty pericarp5 (emp5) mutants in maize (Zea mays). Null mutation of Emp5 results in abortion of embryo and endosperm development at early stages. Emp5 encodes a mitochondrion-targeted DYW subgroup pentatricopeptide repeat (PPR) protein. Analysis of the mitochondrial transcripts revealed that loss of the EMP5 function abolishes the C-to-U editing of ribosomal protein L16 at the rpl16-458 site (100% edited in the wild type), decreases the editing at nine sites in NADH dehydrogenase9 (nad9), cytochrome c oxidase3 (cox3), and ribosomal protein S12 (rps12), and surprisingly increases the editing at five sites of ATP synthase F0 subunit a (atp6), apocytochrome b (cob), nad1, and rpl16. Mutant EMP5-4 lacking the E+ and DYW domains still retains the substrate specificity and editing function, only at reduced efficiency. This suggests that the E+ and DYW domains of EMP5 are not essential to the EMP5 editing function but are necessary for efficiency. Analysis of the ortholog in rice (Oryza sativa) indicates that rice EMP5 has a conserved function in C-to-U editing of the rice mitochondrial rpl16-458 site. EMP5 knockdown expression in transgenics resulted in slow growth and defective seeds. These results demonstrate that Emp5 encodes a PPR-DYW protein that is required for the editing of multiple transcripts in mitochondria, and the editing events, particularly the C-to-U editing at the rpl16-458 site, are critical to the mitochondrial functions and, hence, to seed development in maize.
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| [73] |
Mitochondrial group II introns require the participation of numerous nucleus-encoded general and specific factors to achieve efficient splicing in vivo. Pentatricopeptide repeat (PPR) proteins have been implicated in assisting group II intron splicing. Here, we identified and characterized a new maize seed mutant, defective kernel 37 (dek37), which has significantly delayed endosperm and embryo development. Dek37 encodes a classic P-type PPR protein that targets mitochondria. The dek37 mutation causes no detectable DEK37 protein in mutant seeds. Mitochondrial transcripts analysis indicated that dek37 mutation decreases splicing efficiency of mitochondrial nad2 intron 1, leading to reduced assembly and NADH dehydrogenase activity of complex I. Transmission Electron Microscopy (TEM) revealed severe morphological defects of mitochondria in dek37. Transcriptome analysis of dek37 endosperm indicated enhanced expression in the alternative respiratory pathway and extensive differentially expressed genes related to mitochondrial function. These results indicated that Dek37 is involved in cis-splicing of mitochondrial nad2 intron 1 and is required for complex I assembly, mitochondrial function, and seed development in maize.
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| [74] |
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| [78] |
Seeds of the lethal embryo 1 (lem1) mutant in maize (Zea mays) display a non‐concordant lethal phenotype: whereas the embryo aborts very early, before the transition stage, the endosperm develops almost normally. The mutant was identified in a collection of maize lines that carried the transposon Activation (Ac) at different locations in the genome. Co‐segregation and reversion analysis showed that lem1 was tagged by Ac. The lem1 gene encodes a protein that is highly similar to the rice plastid 30S ribosomal protein S9 (PRPS9). lem1 maps to chromosome 1L and appears to be the only copy of prps9 in the maize genome. Green fluorescent protein (GFP) fusion constructs containing only the putative transit peptide (TP) of LEM1 localize exclusively to the plastids, confirming that the LEM1 protein is a PRP. In contrast, GFP fusion constructs containing the entire LEM1 protein co‐localize to the plastids and to the nucleus, suggesting a possible dual function for this protein. Two alternative, although not mutually exclusive, explanations are considered for the lem phenotype of the lem1 mutant: (i) functional plastids are required for normal embryo development; and (ii) the PRPS9 has an extra‐ribosomal function required for embryogenesis.
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| [79] |
In emb (embryo specific) mutants of maize (Zea mays), the two fertilization products have opposite fates: Although the endosperm develops normally, the embryo shows more or less severe aberrations in its development, resulting in nonviable seed. We show here that in mutant emb8516, the development of mutant embryos deviates as soon as the transition stage from that of wild-type siblings. The basic events of pattern formation take place because mutant embryos display an apical-basal polarity and differentiate a protoderm. However, morphogenesis is strongly aberrant. Young mutant embryos are characterized by protuberances at their suspensor-like extremity, leading eventually to structures of irregular shape and variable size. The lack of a scutellum or coleoptile attest to the virtual absence of morphogenesis at the embryo proper-like extremity. Molecular cloning of the mutation was achieved based on cosegregation between the mutant phenotype and the insertion of a MuDR element. The Mu insertion is located in gene ZmPRPL35-1, likely coding for protein L35 of the large subunit of plastid ribosomes. The isolation of a second allele g2422 and the complementation of mutant emb8516 with a genomic clone of ZmPRPL35-1 confirm that a lesion in ZmPRPL35-1 causes the emb phenotype. ZmPRPL35-1 is a low-copy gene present at two loci on chromosome arms 6L and 9L. The gene is constitutively expressed in all major tissues of wild-type maize plants. Lack of expression in emb/emb endosperm shows that endosperm development does not require a functional copy of ZmPRPL35-1 and suggests a link between plastids and embryo-specific signaling events.
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Ribosome biogenesis is a fundamental cellular process in all cells. Impaired ribosome biogenesis causes developmental defects; however, its molecular and cellular bases are not fully understood. We cloned a gene responsible for a maize (Zea mays) small seed mutant, dek* (for defective kernel), and found that it encodes Ribosome export associated1 (ZmReas1). Reas1 is an AAA-ATPase that controls 60S ribosome export from the nucleus to the cytoplasm after ribosome maturation. dek* is a weak mutant allele with decreased Reas1 function. In dek* cells, mature 60S ribosome subunits are reduced in the nucleus and cytoplasm, but the proportion of actively translating polyribosomes in cytosol is significantly increased. Reduced phosphorylation of eukaryotic initiation factor 2α and the increased elongation factor 1α level indicate an enhancement of general translational efficiency in dek* cells. The mutation also triggers dramatic changes in differentially transcribed genes and differentially translated RNAs. Discrepancy was observed between differentially transcribed genes and differentially translated RNAs, indicating distinct cellular responses at transcription and translation levels to the stress of defective ribosome processing. DNA replication and nucleosome assembly-related gene expression are selectively suppressed at the translational level, resulting in inhibited cell growth and proliferation in dek* cells. This study provides insight into cellular responses due to impaired ribosome biogenesis. © 2016 American Society of Plant Biologists. All Rights Reserved.
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Ribosome biogenesis is a fundamental process in eukaryotic cells. Although Urb2 protein has been implicated in ribosome biogenesis in yeast, the Urb2 domain is loosely conserved between plants and yeast, and the function of Urb2 protein in plants remains unknown. Here, we isolated a maize mutant, designated as urb2, with defects in kernel development and vegetative growth. Positional cloning and transgenic analysis revealed that urb2 encodes an Urb2 domain-containing protein. Compared with the wild-type (WT), the urb2 mutant showed decreased ratios of 60S/40S and 80S/40S and increased ratios of polyribosomes. The pre-rRNA intermediates of 35/33S rRNA, P-A3 and 18S-A3 were significantly accumulated in the urb2 mutant. Transcriptome profiling of the urb2 mutant indicated that ZmUrb2 affects the expression of a number of ribosome-related genes. We further demonstrated that natural variations in ZmUrb2 are significantly associated with maize kernel length. The overall results indicate that, by affecting pre-rRNA processing, the Urb2 protein is required for ribosome biogenesis in maize.© 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.
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PDF(2139 KB)
Collection(s)
表1 5个玉米籽粒相关性状的描述性统计及遗传力表2 5个玉米籽粒性状之间的相关性
图1 5个玉米籽粒相关性状的表型分布图2 不同模型玉米籽粒相关性状的全基因组关联分析表3 5个玉米籽粒相关性状的全基因组关联分析结果及候选基因预测图3 5个玉米籽粒相关性状的条件分析表4 玉米籽粒相关性状的上位性互作分析结果图4 玉米籽粒相关性状候选基因的功能分类/
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