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Title:Genome-wide association mapping of temperature response in agronomically important traits of soybean
Author(s):Nasarudin, Noor Syahira
Advisor(s):Hanzawa, Yoshie
Contributor(s):Lipka, Alexander E.; Nelson, Randall L.
Department / Program:Crop Sciences
Discipline:Crop Sciences
Degree Granting Institution:University of Illinois at Urbana-Champaign
Subject(s):Genome-wide association mapping (GWAS)
seed emergence
abiotic stress
Abstract:Seed emergence and plant growth are important agronomic traits affected by environmental fluctuations. A better understanding of the genetic basis of temperature response in important traits of soybean [Glycine max (L.) Merr.] may contribute to improving seed quality and plant development under temperature stress. Genome-wide association study (GWAS) using high-density and high-quality single nucleotide polymorphisms (SNPs) is a powerful tool to associate markers and important traits. The aims of this study are: 1) to characterize the effects of low and high ambient temperature in soybean seed emergence and plant growth; and 2) to identify the genetic factors regulating soybean response to ambient temperature in seed emergence and growth-related traits. A collection of 440 diverse soybean genotypes and SoySNP50K data were used for GWAS. Seeds were germinated and plants were grown under constant 20°C (low) and 30°C (high) temperature in the Plant Care Facility at University of Illinois, Urbana-Champaign. Seed emergence and plant growth data were analyzed using a best linear unbiased prediction (BLUP) model and subjected to GWAS using 36,499 SNPs. For seed emergence in association panel 1 & 2, only 1 SNP on chromosome 9 was significantly associated with relative mean difference for days to initial emergence. For growth-related traits in AP1, a total of 368 SNP-trait associations were identified with 121 and 247 SNPs were significant at FDR=0.05 and 0.10, respectively. No significant marker-trait association was found for days to seed maturity, no. of mature pod at seed maturity, days from seed set to seed maturity, and days from first to last seed maturity, whereas 72 SNPs were significant for days to flowering, one SNP for internode number of first flower and fifty SNPs for days to seed set. A number of significant associations appeared on other traits: 101 SNPs for no. of trifoliate leaf at flowering. 31 SNPs showed for no. of internodes at flowering, 27 SNPs for plant height at flowering, five SNPs for no. of pod, fifteen SNPs for no. of trifoliate leaf at seed set, 31 SNPs for no. of trifoliate leaf at seed maturity, one SNP for no. of internode at seed maturity, three SNPs for plant height at seed maturity, eleven SNPs for last day to seed maturity, two SNPs for of days from flowering to seed set, and ten SNPs for days from flowering to seed maturity. These identified SNPs will facilitate better understanding of the genetic basis of soybean seed emergence and plant growth under low and high temperature stress.
Issue Date:2016-12-08
Rights Information:Copyright 2016 Noor Syahira Nasarudin
Date Available in IDEALS:2017-03-01
Date Deposited:2016-12

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