Mapping Quantitative Trait Loci for Tolerance to Pythium irregulare in Soybean (Glycine max L.)

Abstract

Pythium root rot is one of the significant diseases of soybean (Glycine max (L.) Merr.) in the United States. The causal agent of the disease is a soil-borne oomycete pathogen Pythium irregulare, the most prevalent and aggressive species of Pythium in North Central United States. However, few studies have been conducted in soybean for the identification of quantitative trait loci (QTL) for tolerance to P. irregulare. In this study, two recombinant inbred line (RIL) populations (designated as POP1 and POP2) were challenged with P. irregulare (isolate CMISO2-5-14) in a greenhouse assay. POP1 and POP2 were derived from ‘E09014’ × ‘E05226-T’ and ‘E05226-T’ × ‘E09088’, and contained 113 and 79 lines, respectively. Parental tests indicated that ‘E05226-T’ and ‘E09014’ were more tolerant than ‘E09088’, while ‘E09088’ was highly susceptible to the pathogen. The disease indices, root weight of inoculation (RWI) and ratio of root weight (RRW) of both populations showed near normal distributions, with transgressive segregation, suggesting the involvement of multiple QTL from both parents contributed to the tolerance. All the lines were genotyped using Illumina Infinium BARCSoySNP6K iSelect BeadChip and yielded 1373 and 1384 polymorphic markers for POP1 and POP2, respectively. Notably, despite high density, polymorphic markers coverage was incomplete in some genomic regions. As such, 28 and 37 linkage groups were obtained in POP1 and POP2, respectively corresponding to the 20 soybean chromosomes. Using RRW, one QTL was identified in POP1 on Chromosome 20 that explained 12.7–13.3% of phenotypic variation. The desirable allele of this QTL was from ‘E05226-T’. Another QTL was found in POP2 on Chromosome 11. It explained 15.4% of the phenotypic variation and the desirable allele was from ‘E09088’. However, no QTL were identified using RWI in either population. These results supported that RRW was more suitable to be used to evaluate P. irregulare tolerance in soybean.

Quantitative Disease Resistance Loci towards Phytophthora sojae and Three Species of Pythium in Six Soybean Nested Association Mapping Populations

“…irregulare are new compared with those reported from two previous studies (Ellis et al, 2013;Stasko et al, 2016). However, there is one potential overlap with chromosome 11 recently reported by Lin et al (2018) from Michigan breeding line E09088. In this study and the previous reports, the identified QDRL were minor, with the exception of QDRL on chromosome 13 (BARC-900926-00961), which explained 17.7% of the phenotypic variance in a cross with Dennison (Ellis et al, 2013).…”

“…Comparison of major and minor quantitative disease resistance loci (QDRL) to Py. However, there is one potential overlap with chromosome 11 recently reported by Lin et al (2018) from Michigan breeding line E09088. sporangiiferum significant at the genome-wide threshold mapped in the nested association mapping (NAM) recombinant inbred line (RIL) population generated from the cross of IA3023 ´ LG05-4832.…”

“…This was followed by mapping quantitative disease resistance loci (QDRL) on chromosomes 4 and 7 in Archer using seed plate assays and cup assays (Urrea et al, 2017). irregulare was mapped to chromosomes 11 and 20 in two separate breeding populations (Lin et al, 2018). irregulare was first mapped in two recombinant inbred line (RIL) populations derived from two populations from a three-way cross OHS 303 ´ (Williams ´ PI 424354) and Dennison ´ (Williams ´ PI 42435) on chromosomes 1, 6, 8, 11, and 13 (Ellis et al, 2013).…”

“…Resistance towards P. sojae has been identified in numerous soybean genotypes; >25 single Rps genes as well as numerous quantitative trait loci (QTL) have been mapped (Dorrance and Schmitthenner, 2000;Wang et al, 2010Wang et al, , 2012bLee et al, 2014;Matthiesen et al, 2016;Schneider et al, 2016;Dorrance, 2018). Although resistance towards Pythium has been identified in several soybean genotypes (Griffin, 1990;Bates et al, 2008;Ellis et al, 2013;Balk, 2014), it has only been mapped towards three species of Pythium to date (Rosso et al, 2008;Ellis et al, 2013;Stasko et al, 2016;Urrea et al, 2017;Lin et al, 2018;Klepadlo et al, 2018). A single R gene was mapped on chromosome 13 for resistance to Py.…”

“…More recently, resistance to Py. irregulare was mapped to chromosomes 11 and 20 in two separate breeding populations (Lin et al, 2018). Similarly, resistance to Py.…”