Identification of the Genomic Region Underlying Seed Weight per Plant in Soybean (Glycine max L. Merr.) via High-Throughput Single-Nucleotide Polymorphisms and a Genome-Wide Association Study

Abstract Background The hundred seed weight (HSW) was one of soybean [Glycine max (L.) Merrill] yield components, and was also especially critical for various soybean food types. In this study, a representative sample consisted of 185 accessions, selected from Northeast China, was tested under six tested environments for determination of quantitative trait nucleotide (QTN) of HSW through genome-wide association study (GWAS). Result A total of 24,180 single nucleotide polymorphisms (SNPs) with minor allele frequency more than 0.2 and missing data less than 3% were utilized to the estimate linkage disequilibrium (LD) level in the tested association panel. Thirty-four association signals were identified to be associated with HSW via GWAS. Among them, nineteen QTN were the novel and another fifteen QTN were overlapped or located near the genomic regions of known HSW QTL. A total of 237 genes, derived from 31 QTN, located near peak SNP for six tested environments, were considered as candidate genes, such as plant growing regulation, hormone metabolism, cell, RNA, protein metabolism, development, starch accumulation, secondary metabolism, signaling, and TCA, some of which have been found to participant in the regulation of HSW. A total of 106 SNPs from 16 candidate genes were significantly associated with HSW in soybean. Conclusions The identified loci with beneficial alleles and the candidate genes might be valuable for the molecular network and MAS of HSW.

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Genome-Wide Association Study (GWAS) for Examining the Genomics Controlling Prickle Production in Red Raspberry (Rubus idaeus L.)

Agronomy ◽

10.3390/agronomy11010027 ◽

2020 ◽

Vol 11 (1) ◽

pp. 27

Author(s):

Archana Khadgi ◽

Courtney A. Weber

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Genomic Region ◽

Rubus Idaeus ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Red Raspberry ◽

Genome Wide ◽

A Genome ◽

Genotype By Sequencing

Red raspberry (Rubus idaeus L.) is an expanding high-value berry crop worldwide. The presence of prickles, outgrowths of epidermal tissues lacking vasculature, on the canes, petioles, and undersides of leaves complicates both field management and harvest. The utilization of cultivars with fewer prickles or prickle-free canes simplifies production. A previously generated population segregating for prickles utilizing the s locus between the prickle-free cultivar Joan J (ss) and the prickled cultivar Caroline (Ss) was analyzed to identify the genomic region associated with prickle development in red raspberry. Genotype by sequencing (GBS) was combined with a genome-wide association study (GWAS) using fixed and random model circulating probability unification (FarmCPU) to analyze 8474 single nucleotide polymorphisms (SNPs) and identify significant markers associated with the prickle-free trait. A total of four SNPs were identified on chromosome 4 that were associated with the phenotype and were located near or in annotated genes. This study demonstrates how association genetics can be used to decipher the genetic control of important horticultural traits in Rubus, and provides valuable information about the genomic region and potential genes underlying the prickle-free trait.

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