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Title:Mapping of brown stem rot resistance, genetic yield gains, and yield impact of soybean cyst nematode
Author(s):Rincker, Keith Franklin
Director of Research:Diers, Brian
Doctoral Committee Chair(s):Diers, Brian
Doctoral Committee Member(s):Nelson, Randall; Hartman, Glen; Bohn, Martin; Lipka, Alexander
Department / Program:Crop Sciences
Discipline:Crop Sciences
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:Ph.D.
Genre:Dissertation
Subject(s):brown stem rot
genetic gain
soybean cyst nematode
fine mapping
genome wide association mapping
soybean
disease resistance
Abstract:Fine Mapping of Resistance Genes from Five Brown Stem Rot Resistance Sources in Soybean Brown stem rot (BSR) of soybean [Glycine max (L.) Merr.] caused by Cadophora gregata (Allington & D.W. Chamb.) T.C. Harr. & McNew, can be controlled effectively with genetic host resistance. Three BSR resistance genes Rbs1, Rbs2, and Rbs3 have been identified and mapped to a large region on chromosome 16. Marker-assisted selection (MAS) will be more efficient and gene cloning will be facilitated with a narrowed genomic interval containing an Rbs gene. The objective of this study was to fine map the positions of Rbs genes from five sources. Mapping populations were developed by crossing the resistant sources 'Bell', PI 84946-2, PI 437833, PI 437970, L84-5873, and PI 86150 with either the susceptible cultivar Colfax or Century 84. Plants identified as having a recombination event near Rbs genes were selected and individually harvested to create recombinant lines. Progeny from recombinant lines were tested in a C. gregata root-dip assay and evaluated for foliar and stem BSR symptom development. Overall, 4,878 plants were screened for recombination and progeny from 52 recombinant plants were evaluated with simple sequence repeat (SSR) genetic markers and assessed for symptom development. Brown stem rot resistance was mapped to intervals ranging from 0.34 to 0.04 Mb in the different sources. In all sources, resistance was fine mapped to intervals inclusive of BARCSOYSSR_16_1114 and BARCSOYSSR_16_1115, which provides further evidence that one locus provides BSR resistance in soybean. Genome-Wide Association Study of Brown Stem Rot Resistance in Soybean across Multiple Populations Genetic resistance to BSR of soybean, has been identified and mapped with biparental populations. Although nearly 400 accessions have been identified with BSR resistance, this trait has been mapped in only 12 sources, and just two, PI84946-2 and PI88788, have been utilized to develop BSR resistant cultivars. Thus, there is a serious need to improve our knowledge of the genetic basis of BSR resistance in soybean so that resistance genes in cultivars can be diversified and markers close to resistance genes can be identified and used in marker-assisted selection (MAS). To this end, we conducted a genome-wide association study (GWAS) to identify novel genomic loci associated with BSR and to gain further insight into a previously-reported chromosome 16 region containing Rbs genes. A total of 52,041 single nucleotide polymorphisms (SNPs) were tested for association with BSR in a set of 4,735 accessions from four diversity panels evaluated for resistance from 1989 to 2003. Using a unified mixed linear model and stepwise model selection, we refined the signals within the Rbs interval on chromosome 16 by finding associations that explain a substantial proportion of the total variation of BSR resistance. In combination with significant GWAS signals found elsewhere in the genome, our study will aid efforts to improve BSR resistance by providing new targets for MAS. Genetic Improvement of U.S. Soybean in Maturity Groups II, III, IV Soybean improvement via plant breeding has been critical for the success of the crop. The objective of this study was to quantify genetic change in yield and other traits that occurred during the past 80 yr of North American soybean breeding in maturity groups (MGs) II, III, and IV. Historic sets of 60 MG II, 59 MG III, and 49 MG IV soybean cultivars, released from 1923 to 2008, were evaluated in field trials conducted in 17 U.S. states and one Canadian province during 2010 to 2011. Averaged over 27 MG II and MG IV and 26 MG III site-years of data, the estimated rates of yield improvement during the 80 yr were 23 kg ha–1 yr–1 for MGs II and III, and 20 kg ha–1 yr–1 for MG IV cultivars. However, a two-segment linear regression model provided a better fit to the data and indicated that the average current rate of genetic yield gain across MGs is 29 kg ha–1 yr–1. Modern cultivars yielded more than old cultivars in all environments, but particularly in high-yielding environments. New cultivars in the historic sets used in this study are shorter in height, mature later, lodge less, and have seeds with less protein and greater oil concentration. Given that on-farm soybean yields in the United States are also increasing at a rate of 29 kg ha–1 yr–1, it can be inferred that continual release of greater-yielding cultivars has been a substantive driver of the U.S. on-farm realized yield increases. Impact of Soybean Cyst Nematode Resistance on Soybean Yield Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) of soybean [Glycine max (L.) Merr.] causes extensive yield loss, and host resistance has been an effective strategy to minimize this loss. However, shifts in SCN population virulence compatibility have resulted from the extensive use of PI 88788 as a source of resistance in the Northern U.S. and has the potential to reduce the effectiveness of this resistance source. The Northern Regional Soybean Cyst Nematode Tests offer a vast amount of yield testing combined with entry resistance screening and characterization of nematode host compatibility. The objectives of this study were to utilize previous yield testing to (i) quantify the impact of resistance as the initial field SCN egg counts increases, (ii) explore effects of maturity group (MG) on the impact of resistance, and (iii) gain insights into the effects of host compatibility on PI 88788 on yield. Yield testing from over 11 years was combined into a single dataset with over 1247 test-environment combinations. The yield advantage of SCN resistant entries increased as initial egg counts increased and a larger advantage was found in early MGs (00-II) than later MGs (III-IV). A yield advantage was documented at environments with an initial egg count of 100 eggs 100 cm-3 soil. At all levels of virulence on PI 88788, breeding lines with resistance from PI 88788 yielded more than susceptible entries. Predictions from this dataset offer a unique view of the impact SCN resistance provides in soybean and relationships among differing levels of virulence on PI 88788.
Issue Date:2016-05-11
Type:Thesis
URI:http://hdl.handle.net/2142/92695
Rights Information:Copyright 2016 Keith Rincker
Date Available in IDEALS:2016-11-10
Date Deposited:2016-08


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