2025 Volume 58 Issue 14 Published: 16 July 2025
  

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    CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    ZHENG MinHua, CHEN Luo, XING JiaLe, XIE YueLan, JIANG XianYa, NIE Shuai, CAI FuGe, WU HaoXiang, LU ZhanHua, SUN Wei, HUO Xing, BAI Song, ZHAO JunLiang, YANG Wu
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    【Objective】Rice blast critically compromises rice production. The genetic enhancement of blast resistance remains challenging due to pathogen variability and limited genetic diversity in breeding parents. This study seeks to accelerate resistance breeding by identifying novel resistance loci through systematic germplasm characterization. 【Method】A panel of 265 sequenced indica rice accessions (including 120 international germplasms and 145 cultivars from South China) underwent field-based blast resistance evaluation. Genome-wide association study (GWAS) was subsequently employed to identify blast resistance quantitative trait loci (QTL). Haplotype effects of these QTL on blast resistance were analyzed, and candidate genes within newly identified QTL regions were predicted using rice genome annotation. 【Result】Field resistance evaluation identified 47 accessions (18 international germplasms and 29 cultivars from South China) exhibiting high resistance to both panicle and leaf blast. GWAS detected nine blast resistance QTL distributed across chromosomes 1, 5, 6, 11, and 12, respectively. Among them, four QTL was co-localized with previously reported blast resistance genes and five QTL were newly identified. Haplotype analysis revealed significant resistance variations associated with peak SNP alleles, with eight QTL showing higher frequency of resistant haplotypes in cultivars from South China compared to international germplasms. Notably, the qPB11 locus demonstrated an inverse distribution pattern, where its resistant haplotype frequency was substantially lower in cultivars from South China (1%) than in international germplasm (16%). Candidate gene analysis within novel QTL regions identified four NBS-LRR disease resistance proteins and four NB-ARC domain-containing proteins, with eight candidate genes clustered within a 27.22-27.35 Mb interval on chromosome 11.【Conclusion】Cultivars from South China exhibit superior blast resistance compared to international germplasms. The high-resistance haplotypes of qPB1-1, qPB1-2, qPB1-3, qPB5, qPB6, qPB12-1, and qLB12/qPB12-2 have been preferentially selected during the genetic improvement of cultivars from South China. Furthermore, the qPB11 locus harbors genes encoding NBS-LRR disease-resistant proteins and NB-ARC domain-containing proteins, representing new potential resistance gene for rice blast disease.

  • CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS
    WUCuiCui, WANGRuoYu, MAChi, HEMeiYue, YINXiaoKang, FENGJiaYi, ZHOUBinHan, JIANGYuFan, JINHanBing, ZHAOLiLi, SUNJi, FANGZhengWu, CHENGLing, ZHUZhanWang, LIUYiKe, ZHANGYingXin, WANGShuPing
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    【Objective】Centromeric retrotransposons (CR) play an important role in maintaining chromosomal stability of Poaceae species. Rye (Secale cereale L. cv. Imperial), a valuable genetic donor for wheat improvement, showed enhanced stress tolerance and disease resistance, the centromeric regions of which are enriched with CR. Screen active rye specific CR (CR of Rye, CRR) and study their transposition patterns under stress conditions, would help elucidate the mechanisms of the possible influence of transposable elements (TEs) transposition on genome stability of rye under stress conditions. 【Method】To identify intact CRR, the rye genome was subjected to de novo annotation of TEs using bioinformatics tools. Semi-quantitative analysis was applied to screen highly expressed CRR in both leaves and roots of rye. Quantitative real-time PCR (qRT-PCR), methylation-specific PCR (MSP), and transposon display (TD) techniques were used to analyze the expression and methylation level, and transposition activity of the screened CRR in leaves and roots of abiotic stressed rye seedlings (at the one-tip-two-leaf stage), including salt, ABA, H2O2, PEG, low temperature, and high temperature. 【Result】Seventeen CRR were identified, and seven have intact structure (CRR1, CRR2, CRR3, CRR4, CRR5, CRR7, and CRR11). Semi-quantitative analysis revealed CRR2, CRR4, and CRR7 were highly expressed in both leaves and roots. Structural analysis of the three CRR indicated that they could encode all the enzymes necessary for TE transposition (reverse transcriptase, ribonuclease H, and integrase), with CRR7 also encoded a Gag protein. Under normal conditions, CRR2, CRR4, and CRR7 were basically expressed, which were upregulated by stress treatments, the methylation level of CRR7 changed most under stressed conditions, followed by CRR2 and CRR4. Additionally, the copy number of the three CRR was dynamically changed under stress conditions. Under different stress conditions, the insertion and excision frequency of CRR was different under different stress conditions, but the overall excision frequency was higher than the insertion frequency.【Conclusion】The higher of the sequence homology between the 5’ and 3’ LTRs of CRR, the higher of the transcriptional activity of CRR; active CRR have basical transcriptional level under normal conditions, the transcription and transposition activity of which were upregulated by stress stimuli, which were primarily regulated by post-transcriptional regulatory mechanisms. Genomic rearrangement might be the main factor affecting the copy number of CRR in stress conditions.