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Title:Overcoming the domestication bottleneck in soybean: mapping domestication traits and using wild soybean to improve diversity
Author(s):Swarm, Stephen Anthony
Director of Research:Nelson, Randall L
Doctoral Committee Chair(s):Nelson, Randall L
Doctoral Committee Member(s):Brown, Patrick J; Diers, Brian W; Ma, Jianxin; Sacks, Erik J
Department / Program:Crop Sciences
Discipline:Crop Sciences
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:Ph.D.
Genre:Dissertation
Subject(s):Soybean
Glycine max
Glycine soja
QTL mapping
Domestication
Genetic diversity
Abstract:QTL Mapping of Domestication-Related Traits Soybean [Glycine max (L.) Merr.] was domesticated in East Asia from the wild progenitor Glycine soja. The domestication process led to many distinct morphological changes that adapt it to cultivation. These include larger seeds, erect growth, larger stem diameter, reduced pod shattering, and altered growth habit. The objective of this study was to identify QTL controlling key domestication-related traits (DRT). A total of 151 RILs from Williams 82 x PI 468916 and 510 RILs from Williams 82 x PI 479752 were utilized for QTL mapping. The lines were genotyped using a genotyping-by-sequencing (GBS) protocol which resulted in nearly 17,000 polymorphic SNP markers. For the eleven traits measured in this study, Haley-Knott regression was used to identify 97 QTL. The number of QTL detected for each trait ranged between 1-3 QTL in the smaller Williams 82 x PI 468916 population and 2-11 QTL in the larger Williams 82 x PI 479752 population. The majority of DRT examined in this study were controlled by minor QTL, with QTL explaining over 50% of the variation only detected for flowering date, maturity date, shattering, and pubescence type. The 97 QTL were distributed across all 20 chromosomes within 36 genomic regions. These findings identify additional QTL not detected in previous studies using smaller populations while also confirming the quantitative nature for several of the important DRT in soybeans. These results may be useful for enabling more effective use of the wild germplasm and to further understand the genetic basis of traits related to soybean domestication. Evaluation of G. soja-Derived Lines The genetic bottleneck caused during the domestication of soybean significantly reduced genetic diversity, as soybean landraces only contain half of the genetic diversity found in G. soja populations. Considering the narrow genetic base found within North American soybean cultivars and the greater genetic diversity present in G. soja, the wild species may represent a rich source of novel diversity to boost genetic gain. The objectives of this research were to identify high-yielding lines derived from G. max x G. soja crosses and characterize patterns of G. soja introgression in those high-yielding lines. A total of 416 G. max x G. soja lines were evaluated, all developed through the USDA soybean breeding program at Urbana, IL. A total of 26 different crosses were represented involving 14 different G. soja accessions and 11 G. max parents. In 2015, yield and other agronomic data were collected on the 416 lines at two locations in Illinois. In 2016, 300 lines were selected and evaluated at 5 locations in Illinois, Missouri, and Nebraska. Lines which regained the yield of the soybean parent were identified within four G. max x G. soja crosses. Two lines from LN97-15076 x LG01-7770 were equivalent in yield to the G. max parent, LN97-15076. Twenty lines derived from Williams 82 were equivalent in yield to the soybean parent, and two lines were significantly higher yielding than Williams 82. On average, G. soja-derived lines contained fewer G. soja SNPs than what would be expected without selection. This indicates that intense phenotypic selection also led to a reduction in overall contribution from the G. soja parent. Within the Williams 82 x PI 479752 cross, regions containing DRT QTL tended to be in close proximity to regions with low frequencies of G. soja alleles. Only two lines had G. soja SNPs within a major shattering QTL on chromosome 16, although 20 lines contained G. soja introgressions within 500 kb of the QTL. High-yielding lines from this study should be good candidates to introduce novel diversity in soybean, especially lines with G. soja introgressions within domestication-related selective sweeps.
Issue Date:2017-07-11
Type:Thesis
URI:http://hdl.handle.net/2142/98344
Rights Information:Copyright 2017 Stephen Swarm
Date Available in IDEALS:2017-09-29
Date Deposited:2017-08


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