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Comprehensive Genome-Wide Association Analysis Reveals the Genetic Basis of Root System Architecture in Soybean.

ABSTRACT: Increasing the understanding genetic basis of the variability in root system architecture (RSA) is essential to improve resource-use efficiency in agriculture systems and to develop climate-resilient crop cultivars. Roots being underground, their direct observation and detailed characterization are challenging. Here, were characterized twelve RSA-related traits in a panel of 137 early maturing soybean lines (Canadian soybean core collection) using rhizoboxes and two-dimensional imaging. Significant phenotypic variation (P < 0.001) was observed among these lines for different RSA-related traits. This panel was genotyped with 2.18 million genome-wide single-nucleotide polymorphisms (SNPs) using a combination of genotyping-by-sequencing and whole-genome sequencing. A total of 10 quantitative trait locus (QTL) regions were detected for root total length and primary root diameter through a comprehensive genome-wide association study. These QTL regions explained from 15 to 25% of the phenotypic variation and contained two putative candidate genes with homology to genes previously reported to play a role in RSA in other species. These genes can serve to accelerate future efforts aimed to dissect genetic architecture of RSA and breed more resilient varieties.

SUBMITTER: Seck W

PROVIDER: S-EPMC7772222 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:IntroductionAvocado (Persea americana) is a highly nutritious fruit gaining worldwide popularity. However, its cultivation is currently reliant on a limited number of cultivars with restricted genetic diversity. This study aims to investigate the genetic diversity and population structure of avocado germplasm and identify genetic loci associated with key fruit quality traits that influence customer preference.MethodsA diversity panel of 110 avocado accessions was analyzed using 4,706 high-quality single nucleotide polymorphisms (SNPs). Genetic diversity and population structure were analyzed using pairwise FST, AMOVA, admixture analysis, and phylogenetic analysis. Genome-wide association studies (GWAS) were conducted targeting nine fruit quality traits using two models: General Linear Model (GLM) with Principal Component Analysis (PCA) and Mixed Linear Model (MLM) with PCA and kinship (PCA + K).ResultsThe analysis revealed three distinct populations corresponding to the three avocado ecotypes: Guatemalan, West Indian, and Mexican. Phylogenetic analysis indicated a closer relationship between the Guatemalan and West Indian races compared to the Mexican race in our Florida germplasm collection. GWAS led to identification of 12 markers within 11 genomic regions significantly associated with fruit quality traits such as fruit color, shape, taste, and skin texture. These markers explained between 14.84% to 43.96% of the phenotypic variance, with an average of 24.63%. Annotation of these genomic regions unveiled candidate genes potentially responsible for controlling these traits.DiscussionThe findings enhance our understanding of genetic diversity and population structure in avocado germplasm. The identified genetic loci provide valuable insights into the genetic basis of fruit quality traits, aiding breeding programs in developing improved avocado cultivars. Marker-assisted selection can accelerate the development of new varieties, promoting a more diverse and resilient avocado market.

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Comprehensive Genome-Wide Association Analysis Reveals the Genetic Basis of Root System Architecture in Soybean.

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