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Identifcation of superior and rare haplotypes to optimize branch number in soybean

Branch number is a key yield-related quantitative trait that directly afects the number of pods and seeds per soybean plant. In this study, an integrated approach with a genome-wide association study (GWAS) and haplotype and candidate gene analyses was used to determine the detailed genetic basis of branch number across a diverse set of soybean accessions. The GWAS revealed a total of eleven SNPs signifcantly associated with branch number across three environments using the fve GWAS models.

Hui Yu, Javad Akhter Bha, Candong Li, Beifang Zhao, Moran Bu, Zhirui Zhang, Tai Guo, Xianzhong Feng

Theoretical and Applied Genetics; April 2024; vol.137; article 93

Key message

Using the integrated approach in the present study, we identifed eleven signifcant SNPs, seven stable QTLs and 20 candidate genes associated with branch number in soybean.

Abstract

Branch number is a key yield-related quantitative trait that directly afects the number of pods and seeds per soybean plant. In this study, an integrated approach with a genome-wide association study (GWAS) and haplotype and candidate gene analyses was used to determine the detailed genetic basis of branch number across a diverse set of soybean accessions. The GWAS revealed a total of eleven SNPs signifcantly associated with branch number across three environments using the fve GWAS models. Based on the consistency of the SNP detection in multiple GWAS models and environments, seven genomic regions within the physical distance of±202.4 kb were delineated as stable QTLs. Of these QTLs, six QTLs were novel, viz., qBN7, qBN13, qBN16, qBN18, qBN19 and qBN20, whereas the remaining one, viz., qBN12, has been previously reported. Moreover, 11 haplotype blocks, viz., Hap4, Hap7, Hap12, Hap13A, Hap13B, Hap16, Hap17, Hap18, Hap19A, Hap19B and Hap20, were identifed on nine diferent chromosomes. Haplotype allele number across the identifed haplotype blocks varies from two to fve, and diferent branch number phenotype is regulated by these alleles ranging from the lowest to highest through intermediate branching. Furthermore, 20 genes were identifed underlying the genomic region of±202.4 kb of the identifed SNPs as putative candidates; and six of them showed signifcant diferential expression patterns among the soybean cultivars possessing contrasting branch number, which might be the potential candidates regulating branch number in soybean. The fndings of this study can assist the soybean breeding programs for developing cultivars with desirable branch numbers.

 

See https://link.springer.com/article/10.1007/s00122-024-04596-y

Figure 1: Marker distribution and density of 200 soybean accessions collected from five accumulated temperature zones of northeastern China. A Genome-wide distribution of 2,715,610 SNP markers that are used for GWAS. B This diagram shows the presence of the 2,715,610 SNPs across twenty soybean chromosomes. Length of chromosomes (Mb) is represented by the horizontal axis, chromosome number is denoted by the vertical axis, and SNP density is depicted by the different colours (number of SNPs per window)

 

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