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.

Keywords: DArT markers; genome-wide association studies (GWAS); grain sorghum; multi-parent advanced generation inter-cross (MAGIC); yield components.

FIGURE 1

Frequency distribution of each phenotypic trait of the MBL population including DTA (days to anthesis), PH (plant height), GY (grain yield), TGW (1000-grain weight), TN (tiller number per meter), and YPP (yield per panicle).

FIGURE 2

Manhattan plots based on rMVP-GWAS program using MBL population with highlighted genes or loci identified for various traits. Vertical dotted bars show genes and loci related to (A) days to anthesis (DTA: Chr3, Chr4 & Chr5); (B) Plant height or dwarfing genes (Dw1: Chr9, Dw2: Chr6, and Dw3: Chr7); (C) Grain yield and Dw3 (Chr7); (D) 1000-grain weight and Dw1 (Chr9); (E) Yield per plant and Dw3 (Chr3 and Chr7). The -log₁₀ (p) values (y-axis) are plotted against the position on each chromosome (x-axis). Each solid circle represents a SNP, and the red dashed line represents the Bonferroni-corrected threshold (p ≤ 0.05).