Development and characterization of a sorghum multi-parent advanced generation intercross (MAGIC) population for capturing diversity among seed parent gene pool

Abstract

Multi-parent advanced generation inter-cross (MAGIC) populations improve the precision of quantitative trait loci (QTL) mapping over biparental populations by incorporating increased diversity and opportunities to reduce linkage disequilibrium among variants. Here, we describe the development of a MAGIC B-Line (MBL) population from an inter-cross among four diverse founders of grain sorghum [Sorghum bicolor (L.) Moench] across different races (kafir, guinea, durra, and caudatum). These founders were selected based on genetic uniqueness and several distinct qualitative features including panicle architecture, plant color, seed color, endosperm texture, and awns. A whole set of MBL (708 F6) recombinant inbred lines (RILs) along with their founders were genotyped using Diversity Arrays Technology (DArTseq) and 5,683 single nucleotide polymorphisms (SNPs) were generated. A genetic linkage map was constructed using a set of polymorphic, quality-filtered markers (2,728 SNPs) for QTL interval-mapping. For population validation, three traits (seed color, plant color and awns) were used for QTL mapping and genome-wide association study (GWAS). QTL mapping and GWAS identified four major genomic regions located across three chromosomes (Chr1, Chr3, and Chr6) that correspond to known genetic loci for the targeted traits. Founders of this population consist of the fertility maintainer (A/B line) gene pool and derived MBL lines could serve as female/seed parents in the cytoplasmic male sterility (CMS) breeding system. The MBL population will serve as a unique genetic and genomic resource to better characterize the genetics of complex traits and potentially identify superior alleles for crop improvement efforts to enrich the seed parent gene pool.

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

“…High resolution mapping is a critical step for the identification of novel genes and narrows down the genetic distance between the candidate genes associated with complex traits in crop plants ( Huang et al, 2015 ; Scott et al, 2020 ; Kumar et al, 2023 ). As we reported earlier ( Kumar et al, 2023 ), the genome-wide LD decayed much more quickly in the MBL compared to a biparental population ( Supplementary Figure S4 ), which is consistent with previous comparisons between biparental and MBL populations ( Boyles et al, 2017a ). Based on the previous mapping studies, the MAGIC populations are more efficient to narrow down the genomic regions compared to biparental populations ( Huang et al, 2012 ; Kumar et al, 2023 ).…”

“…MBL population was developed from crosses between four founder lines SC630 (PI533937), SC605 (PI534096), BTx642 (PI656029), and BTxARG-1 (PI561072). These founders were selected to capture genetic diversity across multiple botanical races (SC630 = kafir, SC605 = guinea, BTx642 = durra, and BTxARG-1 = caudatum) as well as broad phenotypic variation across various qualitative, agronomic and yield related traits ( Kumar et al, 2023 ). In addition, the MBL was genetically characterized for some well-known, heritable traits such as seed color, plant color, and awns using QTL mapping and GWAS.…”

“…In addition, the MBL was genetically characterized for some well-known, heritable traits such as seed color, plant color, and awns using QTL mapping and GWAS. Full details on the development and initial characterization of the MBL panel are described by Kumar et al (2023) .…”

“…The MBL population was previously sequenced as described in Kumar et al (2023) . Briefly, DNA was extracted by Intertek (Alnarp, Sweden) from desiccated leaf punches collected from individual RILs and four parents at Florence, SC field site, with most plants at the grain filling stage.…”

“…In the present study, a recently developed MBL population was leveraged to mine the B-line (female) parent gene pool for novel and favorable genetic variation ( Kumar et al, 2023 ). A set of polymorphic, quality-filtered markers (3,751 SNPs) were generated using Diversity Arrays Technology sequencing (DArTseq).…”