Genome-Wide Association Study of Seed Morphology Traits in Senegalese Sorghum Cultivars

Abstract

Sorghum is considered the fifth most important crop in the world. Despite the potential value of Senegalese germplasm for various traits, such as resistance to fungal diseases, there is limited information on the study of sorghum seed morphology. In this study, 162 Senegalese germplasms were evaluated for seed area size, length, width, length-to-width ratio, perimeter, circularity, the distance between the intersection of length & width (IS) and center of gravity (CG), and seed darkness and brightness by scanning and analyzing morphology-related traits with SmartGrain software at the USDA-ARS Plant Science Research Unit. Correlations between seed morphology-related traits and traits associated with anthracnose and head smut resistance were analyzed. Lastly, genome-wide association studies were performed on phenotypic data collected from over 16,000 seeds and 193,727 publicly available single nucleotide polymorphisms (SNPs). Several significant SNPs were found and mapped to the reference sorghum genome to uncover multiple candidate genes potentially associated with seed morphology. The results indicate clear correlations among seed morphology-related traits and potential associations between seed morphology and the defense response of sorghum. GWAS analysis listed candidate genes associated with seed morphologies that can be used for sorghum breeding in the future.

Genome-Wide Association Analysis Uncovers Genes Associated with Resistance to Head Smut Pathotype 5 in Senegalese Sorghum Accessions

“…In cluster analysis, seed weight clustered with other seed size-related traits, as expected based on our previous work (Table 3) [23]. The head smut incidence rate is grouped with two seed shape-related traits and the seedling head smut spot appearance rate [18,19].…”

“…Pearson's correlation analysis in Senegalese sorghum accessions revealed an intriguing link between head smut incidence rate (P5) and seed morphology traits [23], including newly measured seed weight (Table 2). Notably, larger seeds (area, perimeter, width, distance between IS, and CG) exhibited positive correlations with P5 incidence, suggesting greater susceptibility.…”

“…This study evaluates the response of 153 Senegalese sorghum accessions to a newly identified pathotype 5 of S. reilianum through syringe needle inoculation (hypodermic injection). Furthermore, we investigated potential associations between head smut resistance and previously reported data in seed morphology and the seedling screening method established by Craig and Frederiksen [17][18][19]23]. To investigate these connections further, seed weight was measured for 59 lines, allowing us to assess any potential linkage between this trait and head smut susceptibility as well.…”

Genome-wide analysis for root and leaf architecture traits associated with drought tolerance at the seedling stage in a highly ecologically diverse wheat population

“…This precise phenotyping that links to genotypic data in association analyses will facilitate the identification of a specific set of QTLs for complex traits [60] . The ImageJ was previously used to identify significant SNPs associated with target traits (e.g., root angle in wheat) in QTL and GWAS studies No shared markers were found between leaf and root traits [53] , [61] , [62] , [63] .…”

Multi-genome comprehensive identification of SSR/SV and development of molecular markers database to serve Sorghum bicolor (L.) breeding

“…Sorghum bicolor (L.) Moench, as an annual C4 herbaceous plant of the family poaceae, has many advantages such as drought tolerance, salt tolerance, barren tolerance, waterlogging tolerance, and strong photosynthetic ability [ 1 – 3 ]. Because of its strong environmental adaptability and excellent agronomic traits, it is not only used as a model plant for plant breeding research, but also used in industrial fields such as chinese hard liquor making, sugar making and bioenergy, which makes it the fifth important cereal in the world and widely planted in hundreds of countries and regions such as tropical, subtropical and temperate zones [ 4 – 6 ]. Diverse growth environments and widespread farm lines have shaped the nucleic acid diversity of the sorghum population gene pool [ 7 ].…”