Single nucleotide polymorphisms facilitate distinctness‐uniformity‐stability testing of soybean cultivars for plant variety protection

Abstract

Plant variety protection (PVP), or plant breeders’ rights, provides intellectual property protection (IPP) for cultivars. Technical requirements are distinctness, uniformity, and stable (DUS) reproduction. However, field trials are increasingly resource demanding and potentially inconclusive for soybean (Glycine max [L.] Merr.). Our objective was to establish methodologies using molecular markers to facilitate DUS testing while maintaining current IPP levels. We determined that DNA from 10–15 bulked plants represented cultivar genotype. Single nucleotide polymorphism (SNP) data were highly robust in the face of missing and mistyped data; concordances among five laboratories were >.9888. We used SNP, morphological, physiological, and pedigree information to examine 322 publicly available cultivars including 187 with PVPs. Associations among cultivars following multivariate analyses of genetic distances from SNP data and from pedigree kinship data were very similar. A SNP similarity of 98.6% was the maximum at which cultivars also differed for morphological characteristics. Many (38%) cultivar pairs with members >90% SNP similarity expressed different morphologies with SNP similarities ranging 96–98.6%. Of cultivars <96% SNP similar, only a single pair differed by a single morphological difference; all others differed by more than two morphological characteristics. A SNP similarity of 96% between soybean cultivars represents an initial and conservative point of demarcation between cultivars that have morphological differences and those that do not. Chronological monitoring of pedigree–kinship and SNP similarities showed little evidence that a lack of genetic diversity in F2 breeding populations contributed to challenges in DUS among U.S. soybean cultivars.

Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research

“…This study showed that the BARCSoySNP6K assay was able to discriminate accessions among landrace, elites and wild soybean as we predicated. Similarly, Liu et al (2017) found that associations among 577 Chinese and US soybean cultivars utilizing the 6K reflected the geographical origins and pedigrees of the cultivars, showing no indication of ascertainment bias within or among these sets of soybean germplasm, similar results were also reported by Achard et al (2020).…”

“…For example, Qi et al (2014) generated 33.10 Gb of data by GBS in soybean, the average sequencing depth was greater than 429 for the two parents, and 3.929 for each of 149 lines, the resulting linkage maps included 5308 markers on 20 linkage groups, of these markers, in total, 3231 had unique genotypic profiles among the lines, the remaining 2077 markers co-segregated with one of the 3231 SNPs in the population. Li et al (2015) analyzed three wheat RIL populations using reads from GBS and constructed genetic maps containing 28 644 SNPs, of these, approximately 13% (3757) had unique segregation patterns in the population, the remaining 87% (24 887 SNP selection bias or ascertainment bias can result from the selection of highly discriminating SNPs utilizing one set of germplasm, but which might then be found to be less usefully discriminating among another unrelated set of germplasm (Achard et al, 2020). For the initial discovery of the SNPs to be included in the SoySNP50K assay, a set of eight genotypes, including six diverse cultivated and two wild soybean genotypes, were sequenced (Song et al, 2013).…”

“…SNP selection bias or ascertainment bias can result from the selection of highly discriminating SNPs utilizing one set of germplasm, but which might then be found to be less usefully discriminating among another unrelated set of germplasm (Achard et al ., 2020). For the initial discovery of the SNPs to be included in the SoySNP50K assay, a set of eight genotypes, including six diverse cultivated and two wild soybean genotypes, were sequenced (Song et al ., 2013).…”

“…Zhang et al (2018) used the markers from 6K and other sources to develop advanced breeding lines carrying different aphidresistance gene(s), and three breeding lines pyramided with multiple aphid-resistance genes, their resistance to diverse and dynamic aphid populations is expected to be strong and durable across geographic regions. Achard et al (2020) analyzed 6K assay data for 322 soybean cultivars released during a three decadal period and granted plant variety protection. They concluded that the methodology of using molecular data from the 6K meets the criteria of maintaining existing levels of intellectual property protection.…”

High-density linkage map reveals QTL for Type-I seed coat cracking in RIL population of soybean [Glycine max (L.) Merr.]

“…A total of 20,046 SNPs showed polymorphism between parental cultivars. The low polymorphism found between the parental lines might be due to the reduced genetic diversity existed among soybean cultivars that resulted as a consequence of domestication and development of commercial varieties (Li et al 2013;Achard et al 2020). The genetic map construction and QTL analysis were performed using the polymorphic markers in QTL IciMapping Ver.…”