Discovering useful genetic variation in the seed parent gene pool for sorghum improvement

Abstract

Multi-parent populations contain valuable genetic material for dissecting complex, quantitative traits and provide a unique opportunity to capture multi-allelic variation compared to the biparental populations. A multi-parent advanced generation inter-cross (MAGIC) B-line (MBL) population composed of 708 F6 recombinant inbred lines (RILs), was recently developed from four diverse founders. These selected founders strategically represented the four most prevalent botanical races (kafir, guinea, durra, and caudatum) to capture a significant source of genetic variation to study the quantitative traits in grain sorghum [Sorghum bicolor (L.) Moench]. MBL was phenotyped at two field locations for seven yield-influencing traits: panicle type (PT), days to anthesis (DTA), plant height (PH), grain yield (GY), 1000-grain weight (TGW), tiller number per meter (TN) and yield per panicle (YPP). High phenotypic variation was observed for all the quantitative traits, with broad-sense heritabilities ranging from 0.34 (TN) to 0.84 (PH). The entire population was genotyped using Diversity Arrays Technology (DArTseq), and 8,800 single nucleotide polymorphisms (SNPs) were generated. A set of polymorphic, quality-filtered markers (3,751 SNPs) and phenotypic data were used for genome-wide association studies (GWAS). We identified 52 marker-trait associations (MTAs) for the seven traits using BLUPs generated from replicated plots in two locations. We also identified desirable allelic combinations based on the plant height loci (Dw1, Dw2, and Dw3), which influences yield related traits. Additionally, two novel MTAs were identified each on Chr1 and Chr7 for yield traits independent of dwarfing genes. We further performed a multi-variate adaptive shrinkage analysis and 15 MTAs with pleiotropic effect were identified. The five best performing MBL progenies were selected carrying desirable allelic combinations. Since the MBL population was designed to capture significant diversity for maintainer line (B-line) accessions, these progenies can serve as valuable resources to develop superior sorghum hybrids after validation of their general combining abilities via crossing with elite pollinators. Further, newly identified desirable allelic combinations can be used to enrich the maintainer germplasm lines through marker-assisted backcross breeding.

Identification of pleiotropic loci mediating structural and non-structural carbohydrate accumulation within the sorghum bioenergy association panel using high-throughput markers

“…The use of the MLM further provides shrinkage to the model such that potential false positives due to shared ancestry are no longer significant. An MLM can be described using Henderson’s matrix notation ( Kumar et al, 2023 ) as follows:…”

“…Genome-wide association studies (GWAS) identify the association between molecular markers and quantitative traits ( Zhu et al., 2008 ). Single nucleotide polymorphisms (SNPs) associated with a variety of phenotypic traits have been identified through GWAS using landraces, diverse accessions, or genetic mapping populations of sorghum, including traits related to plant architecture ( Morris et al., 2013 ; Zhao et al., 2016 ; Hu et al., 2019 ; Kumar et al., 2023 ), agronomy ( Rhodes et al., 2014 ; Boyles et al., 2017 ; Chopra et al., 2017 ; Li et al., 2018 ; Hu et al., 2019 ; Boatwright et al., 2022a ; Kumar et al., 2023 ), bioenergy ( Murray et al., 2008a and Murray et al., 2009 ; Brenton et al., 2016 ; Boyles et al., 2017 , 2019 ; Souza et al., 2021 ), and biomass and its compositional traits ( Brenton et al., 2016 ; Boatwright et al., 2022b ).…”