Characterizing resistance to soybean cyst nematode in PI 494182, an early maturing soybean accession

Abstract

The soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) generates more damage to soybean [Glycine max (L.) Merr.] than any other parasite in most soybeanproducing countries. The use of SCN-resistant cultivars remains the most effective method to limit losses caused by SCN. The SCN-resistant accession PI 88788 has been used almost exclusively to control SCN over the past decades, inducing a shift in nematode virulence to overcome the resistance. Furthermore, PI 88788 and other sources of resistance characterized to date belong to maturity groups (MGs) III and higher, making them less attractive to develop early maturing soybean varieties (MGs 0-000). In this work, we performed a quantitative trait loci (QTL) analysis of the SCNresistant soybean accession PI 494182 (MG 0). A recombinant inbred lines (RILs) population ('Costaud' × PI 494182) segregating for SCN resistance was challenged with SCN (H. glycines [HG] type 0) and genotyped via genotyping-by-sequencing (GBS) to produce a genetic map. Six resistance QTL were identified, including a potentially new resistance locus on chromosome 07. A subset of the RIL population was confronted to a HG type 2.5.7 SCN population and some of these exhibited resistance toward this type. Whole-genome sequencing of PI 494182 and Costaud allowed us to determine the alleles and their copy number for three candidate genes: GmSNAP11, GmSNAP18 (Rhg1), and GmSHMT08 (Rhg4). Finally, we determined that selecting for PI 494182 alleles at some SCN-resistance QTL could entail linkage drag (decrease in protein concentration and 100-seed weight, increase in oil concentration). This work provides useful markers for introgressing SCN resistance in early maturing soybean varieties.

PATRIOT: A Pipeline for Tracing Identity-by-Descent for Chromosome Segments to Improve Genomic Prediction in Self-Pollinating Crop Species

“…The PATRIOT framework facilitates the identification of lines for breeding purposes that have favorable genes linked in coupling, as well as in situations where breaking the linkage drag is imperative. For example, SCN resistance from PI494182 was determined to carry a risk of linkage drag ( St-Amour et al, 2020 ). Likewise, SCN resistance from the commonly used donor PI88788 was initially associated with considerable linkage drag ( Cregan et al, 1999 ).…”

A Broad Review of Soybean Research on the Ongoing Race to Overcome Soybean Cyst Nematode

“…Researchers also identified a new resistance QTL on Chr. 07 [ 58 ]. A genetic linkage map of the RIL population from a cross between the resistant line PI 494,182 (Suzuhime), and the early maturity cultivar Costaud (MG 000) led to the identification of six significant QTLs (CSqSCN-1-6) correlated with SCN resistance.…”

High‐throughput NGS‐based genotyping and phenotyping: Role in genomics‐assisted breeding for soybean improvement

“…In this regard, NGS has played a critical role by rapidly identifying the plant lines in which the linkage between undesirable and desirable genes has broken due to recombination process. In one example, NGS was used to identify the recombinants in which the linkage between a favorable allele conferring SCN resistance and a deleterious gene affecting seed quality and 100‐seed weight was broken (St‐Amour et al, 2020). The wild unadapted genotype (PI 494182) used as donor parent possesses the favorable and the unfavorable alleles in coupling phase; hence, the deep NGS sequencing carried on a bigger sized segregation population within the target region identified a recombinant individual in which the linkage had been broken (St‐Amour et al, 2020).…”

“…In one example, NGS was used to identify the recombinants in which the linkage between a favorable allele conferring SCN resistance and a deleterious gene affecting seed quality and 100‐seed weight was broken (St‐Amour et al, 2020). The wild unadapted genotype (PI 494182) used as donor parent possesses the favorable and the unfavorable alleles in coupling phase; hence, the deep NGS sequencing carried on a bigger sized segregation population within the target region identified a recombinant individual in which the linkage had been broken (St‐Amour et al, 2020). In such cases, if the breeders know the functional polymorphism(s) for the desirable and undesirable genes, it would be very easy to identify lines/genotypes in which linkage drag has been broken by recombination event.…”