GWAS and bulked segregant analysis reveal the loci controlling growth habit-related traits in cultivated peanut (Arachis hypogaea L.)

Authors: LI, LI - Auburn University; CUI, SHUNLI - Agricultural University Of Hebei; Dang, Phat; YANG, XINLEI - Auburn University; LIU, LIFENG - Agricultural University Of Hebei; CHEN, CHARLES - Auburn University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/5/2022
Publication Date: 5/27/2022
Citation: Li, L., Cui, S., Dang, P.M., Yang, X., Liu, L., Chen, C. 2022. GWAS and bulked segregant analysis reveal the loci controlling growth habit-related traits in cultivated peanut (Arachis hypogaea L.). Biomed Central (BMC) Genomics. 23,403. https://doi.org/10.1186/s12864-022-08640-3.
DOI: https://doi.org/10.1186/s12864-022-08640-3

Interpretive Summary: Peanut is a grain legume crop that originated from South America and is now grown around the world. Peanut growth habit affects the variety’s adaptability, planting patterns, mechanized harvesting, disease resistance, and yield. To understand the genetic architecture of the peanut growth habit, we decomposed it into five traits related to how the branches grow above ground. To identify genetic components associated with peanut growth habit-related traits, we combined two novel genomics methods, genome-wide association analysis (GWAS) and bulked segregant analysis sequencing (BSA-seq), to pinpoint relative locations on the peanut genome utilizing 103 lines of the U.S. mini core germplasm collection. Single nucleotide polymorphisms (SNPs) or base-pair differences of the peanut lines revealed that many small components for these traits are distributed among 15 chromosomes associating a total of 597 genes that maybe involved. One important trait called lateral branching angle (LBA) was associated with a genomics region on the B05 chromosome with four candidate genes that are involved in plant growth and development. Research results provide molecular targets for molecular breeding approach to develop peanut varieties with agronomic beneficial peanut growth habits.

Technical Abstract: Peanut (Arachis hypogaea L.) is a grain legume crop that originated from South America and is now grown around the world. Peanut growth habit affects the variety’s adaptability, planting patterns, mechanized harvesting, disease resistance, and yield. To understand the genetic architecture of the peanut growth habit, we decomposed it into five related traits: lateral branch angle (LBA), main stem height (MSH), lateral branch height (LBL), extent radius (ER), and the index of plant type (IOPT). To map the quantitative trait loci (QTL) associated with peanut growth habit-related traits, we combined the genome-wide association analysis (GWAS) and bulked segregant analysis sequencing (BSA-seq) methods. GWAS was performed with 17,223 single nucleotide polymorphisms (SNPs) in 103 accessions of the U.S. mini core collection genotyped using an Affymetrix version 2.0 SNP array. With a total of 12,342 high-quality polymorphic SNPs, and 90 suggestive and significant SNPs associated with five growth habit-related traits, these SNPs were distributed among 15 chromosomes. A total of 597 candidate genes were associated that may have important roles in biological processes, hormone signaling, growth, and development. BSA-seq coupled with specific length amplified fragment sequencing (SLAF-seq) method was used to find the association with LBA, an important trait of the peanut growth habit. A 4.08 Mb genomic region on B05 was associated with LBA. Based on the LD decay distance, we narrowed down and confirmed the region within the 160 kb region (144,193,467-144,513,467) on B05. Four candidate genes in this region were involved in plant growth. The results of SNPs and candidate genes identification provide molecular targets for application in marker assisted selection for peanut growth habits.