Identification of genomic loci conferring broad-spectrum resistance to multiple nematode species in exotic soybean accession PI 567305.

KEY MESSAGE: Genetic analysis identified a unique combination of major QTL for resistance to important soybean nematodes concurrently present in a single soybean accession, which has not been reported earlier. An exotic soybean [Glycine max (L.) Merr.] accession, PI 567305, was reported to be highly resistant to three important nematode species, soybean cyst (SCN), root-knot (RKN), and reniform (RN) nematodes. However, genetic basis controlling broad-spectrum resistance in this germplasm has not been investigated. We report results of genetic analysis to identify genomic loci conferring resistance to these nematode species. A bi-parental population consisting of 242 F8-derived recombinant inbred lines (RILs) was developed from a cross of a nematode susceptible cultivar, Magellan, and resistant accession, PI 567305. The RILs were phenotyped for nematode resistance to three SCN HG types. They were genotyped using the Infinium SoySNP6K BeadChips and genotype-by-sequencing (GBS) methods in an attempt to evaluate the cost-effectiveness and efficiency of these two genotyping platforms. Genetic analysis confirmed the major QTL on chromosomes (Chrs) 10 and 18 with broad-spectrum resistance to the three nematodes present in this germplasm. Haplotype and copy number variation analyses of SCN resistance QTL indicated that PI 567305 has a different haplotype, which is associated with likely a unique SCN resistance mechanism different from Peking- or PI 88788-type resistance. The evaluations of both Infinium Beadchip- and GBS-based genotyping technologies provided comprehensive insights for researchers to choose a cost-effective and efficient platform for QTL mapping and for other genomic studies in soybeans.

Genetic architecture of cyst nematode resistance revealed by genome-wide association study in soybean.

BACKGROUND: Bi-parental mapping populations have been commonly utilized to identify and characterize quantitative trait loci (QTL) controlling resistance to soybean cyst nematode (SCN, Heterodera glycines Ichinohe). Although this approach successfully mapped a large number of SCN resistance QTL, it captures only limited allelic diversity that exists in parental lines, and it also has limitations for genomic resolution. In this study, a genome-wide association study (GWAS) was performed using a diverse set of 553 soybean plant introductions (PIs) belonging to maturity groups from III to V to detect QTL/genes associated with SCN resistance to HG Type 0. RESULTS: Over 45,000 single nucleotide polymorphism (SNP) markers generated by the SoySNP50K iSelect BeadChip (http// www.soybase.org ) were utilized for analysis. GWAS identified 14 loci distributed over different chromosomes comprising 60 SNPs significantly associated with SCN resistance. Results also confirmed six QTL that were previously mapped using bi-parental populations, including the rhg1 and Rhg4 loci. GWAS identified eight novel QTL, including QTL on chromosome 10, which we have previously mapped by using a bi-parental population. In addition to the known loci for four simple traits, such as seed coat color, flower color, pubescence color, and stem growth habit, two traits, like lodging and pod shattering, having moderately complex inheritance have been confirmed with great precision by GWAS. CONCLUSIONS: The study showed that GWAS can be employed as an effective strategy for identifying complex traits in soybean and for narrowing GWAS-defined genomic regions, which facilitates positional cloning of the causal gene(s).

Identification of positive yield QTL alleles from exotic soybean germplasm in two backcross populations.

Increasing seed yield is an important breeding goal of soybean [Glycine max (L.) Merr.] improvement efforts. Due to the small number of ancestors and subsequent breeding and selection, the genetic base of current soybean cultivars in North America is narrow. The objective of this study was to map quantitative trait loci (QTL) in two backcross populations developed using soybean plant introductions as donor parents. The first population included 116 BC(2)F(3)-derived lines developed using "Elgin" as the recurrent parent and PI 436684 as the donor parent (E population). The second population included 93 BC(3)F(3)-derived lines developed with "Williams 82" as the recurrent parent and PI 90566-1 as the donor parent (W population). The two populations were evaluated with 1,536 SNP markers and during 2 years for seed yield and other agronomic traits. Genotypic and phenotypic data were analyzed using the programs MapQTL and QTLNetwork to identify major QTL and epistatic QTL. In the E population, two yield QTL were identified by both MapQTL and QTLNetwork, and the PI 436684 alleles were associated with yield increases. In the W population, a QTL allele from PI 90566-1 accounted for 30 % of the yield variation; however, the PI region was also associated with later maturity and shorter plant height. No epistasis for seed yield was identified in either population. No yield QTL was previously reported at the regions where these QTL map indicating that exotic germplasm can be a source of new alleles that can improve soybean yield.

Planting Date and Cultivar Effects on Soybean Yield, Seed Quality, and Phomopsis sp. Seed Infection.

Incidence of Phomopsis seed decay is frequently high and quality low in seed from early-maturing maturity group III and IV soybean cultivars planted in early to mid-April in the southern United States. Cultivars resistant to this disease have not been available until the recent release of germ plasm lines SS 93-6012 and SS 93-6181. Our objective was to determine the effects of planting dates with these lines and one Phomopsis seed decay-susceptible soybean cultivar, Asgrow 3834, on seed infection by Phomopsis spp. and on yield and the correlation between percentage of Asgrow 3834 infected with Phomopsis spp. and seed quality. Generally, yields averaged over years were significantly greater for mid-April than mid-June plantings, and yields of cultivars were similar within a planting date. Soybean lines SS 93-6012 and SS 93-6181 were highly resistant to Phomopsis seed decay compared with the susceptible cultivar, Asgrow 3834. There was a significant, negative correlation between germination of seed from mid-April plantings of Asgrow 3834 and percentage of these seed infected with Phomopsis spp. Moreover, there were significant correlations between fatty acid composition of Asgrow 3834 seed and the percentage of these seed infected with Phomopsis spp. This altered composition of fatty acids may be responsible for reduced quality of oil derived from seed infected with this fungus. Phomopsis seed decay-resistant soybean lines SS 93-6012 and SS 93-6181 should be useful in breeding programs focused on developing high-yielding cultivars resistant to this disease.

Soybean Cultivar and Foliar Fungicide Effects on Phomopsis sp. Seed Infection.

Phomopsis seed decay (PSD) caused by Phomopsis spp. can be severe when soybean seed producers in the southern United States use the early soybean production system (ESPS) to avoid late-July through early-September drought damage to soybean. The usefulness of this production system would be greater if developing seed could be protected from PSD by foliar application of fungicides or by planting Phomopsis spp.-resistant soybean lines. The objective of this research was to determine the affects of the fungicides benomyl and azoxystrobin applied to soybean, at various times, on percent Phomopsis spp. infection of seed in Asgrow 3834, a PSD-susceptible cultivar, and SS93-6012, a PSD-resistant soybean line, planted in mid-April. The percent Phomopsis spp. infection of Asgrow 3834 seed averaged over years was significantly less for the benomyl (0.28 kg a.i. ha-1) applied at R3 + R5 treatment (48.6% seed infection) than the control (52.8% seed infection) and significantly greater for the azoxystrobin (0.17 kg a.i. ha-1) applied at R3 + R5 treatment (61.6% seed infection) than the control (52.8% seed infection). This method of managing PSD will not be acceptable to soybean growers. The percent of Phomopsis spp. infection of Asgrow 3834 seed averaged over years (52.8% seed infection) was significantly greater than for line SS93-6012 (2.8% seed infection). There were no differences in percent Phomopsis spp. infection of SS93-6012 seed between the control (2.8% seed infection) and benomyl treatment (4.0% seed infection). The most effective method for PSD management was to plant a resistant soybean line. Line SS93-6012 will be useful in breeding programs focused on developing high yielding PSD-resistant cultivars.

A Revised Classification Scheme for Genetically Diverse Populations of Heterodera glycines.

Heterodera glycines, the soybean cyst nematode, is a major yield-limiting pathogen in most soybean production areas worldwide. Field populations of H. glycines exhibit diversity in their ability to develop on resistant soybean cultivars. Since 1970, this diversity has been characterized by a bioassay used to assign a race classification to a population. The value of the race scheme is reflected in the number and quality of resistant soybean cultivars that have been developed and released by soybean breeders and nematologists working in concert. However, the race scheme also has been misapplied as a means of studying H. glycines genotypes, in part due to the use of the term "race." For fungal and bacterial pathogen species, "race" can theoretically be applied to individuals of a population, thus allowing inference of individual genotypes. Application of a race designation to an individual egg or second-stage juvenile (J2) of H. glycines is not possible because a single J2 cannot be tested on multiple hosts. For other nematode species, "race" is defined by host ranges involving different plant species, whereas the H. glycines race test involves a set of lines of the same plant species. Nonetheless, because H. glycines populations vary in genetic diversity, and this variation has implications for management strategies, a mechanism is needed for documenting and discussing population differences. The HG Type scheme described herein avoids the implication of genetic uniformity or predictability in contrast to the way the race scheme has been used.

Pooled analysis of data from multiple quantitative trait locus mapping populations.

Quantitative trait locus (QTL) analysis on pooled data from multiple populations (pooled analysis) provides a means for evaluating, as a whole, evidence for existence of a QTL from different studies and examining differences in gene effect of a QTL among different populations. Objectives of this study were to: (1) develop a method for pooled analysis and (2) conduct pooled analysis on data from two soybean mapping populations. Least square interval mapping was extended for pooled analysis by inclusion of populations and cofactor markers as indicator variables and covariate variables separately in the multiple linear models. The general linear test approach was applied for detecting a QTL. Single population-based and pooled analyses were conducted on data from two F(2:3) mapping populations, Hamilton (susceptible) x PI 90763 (resistant) and Magellan (susceptible) x PI 404198A (resistant), for resistance to soybean cyst nematode (SCN) in soybean. It was demonstrated that where a QTL was shared among populations, pooled analysis showed increased LOD values on the QTL candidate region over single population analyses. Where a QTL was not shared among populations, however, the pooled analysis showed decreased LOD values on the QTL candidate region over single population analyses. Pooled analysis on data from genetically similar populations may have higher power of QTL detection than single population-based analyses. QTLs were identified by pooled analysis on linkage groups (LGs) G, B1 and J for resistance to SCN race 2 whereas QTLs on LGs G, B1 and E for resistance to SCN race 5 in soybean PI 90763 and PI 404198A. QTLs on LG G and B1 were identified in both PI 90763 and PI 404198A whereas QTLs on LG E and J were identified in PI 90763 only. QTLs on LGs G and B1 for resistance to race 2 may be the same or closely linked with QTLs on LG G and B1 for resistance to race 5, respectively. It was further demonstrated that QTLs on G and B1 carried by PI 90763 were not significantly different in gene effect from QTLs on LGs G and B1 in PI 404198A, respectively.

Identification of QTLs associated with resistance to soybean cyst nematode races 2, 3 and 5 in soybean PI 90763.

Soybean cyst nematode (SCN) is a major soybean pest throughout the soybean growing regions in the world, including the USA. Soybean PI 90763 is an important SCN resistance source. It is resistant to several SCN populations including races 2, 3 and 5. But its genetics of resistance is not well known. The objectives of this study were to: (1) confirm quantitative trait loci (QTLs) for resistance to SCN race 3 in PI 90763 and (2) identify QTLs for resistance to SCN races 2 and 5. QTLs were searched in Hamilton x PI 90763 F(2:3)populations using 193 polymorphic simple sequence repeats (SSRs) covering 20 linkage groups (LGs). QTLs for resistance to SCN were identified on LGs A2, B1, E, G, J and L. The same QTL was suggested for resistance to different SCN races where their 1-LOD support intervals of QTL positions highly overlapped. The QTL on LG G was associated with resistance to races 2, 3 and 5. The QTL on LG B1 was associated with resistance to races 2 and 5. The QTL on LG J was associated with resistance to races 2 and 3. The QTLs on LGs A2 and L were associated with resistance to race 3. The QTL on LG E was associated with resistance to race 5. We conclude that LGs A2 and B1 may represent an important distinction between resistance to SCN race 3 and resistance to SCN races 2 and 5 in soybean.