Evolution and selection of Rhg1, a copy‐number variant nematode‐resistance locus. Issue 8 (30th March 2015)

• Record Type: Journal Article
• Authors: Lee, Tong Geon; Kumar, Indrajit; Diers, Brian W.; Hudson, Matthew E.
• Is Part Of: Molecular ecology. Volume 24:Issue 8(2015)
• Page Start: 1774
• Page End: 1791
• Publication Date: 2015-03-30
• Subjects: Molecular ecology -- Periodicals; Molecular population biology -- Periodicals; 576
• DOI: 10.1111/mec.13138
• Languages: English
• ISSNs: 0962-1083

Abstract

<abstract abstract-type="main" id="mec13138-abs-0001"> <title>Abstract</title> <p>The soybean cyst nematode (SCN) resistance locus <italic>Rhg1</italic> is a tandem repeat of a 31.2 kb unit of the soybean genome. Each 31.2‐kb unit contains four genes. One allele of <italic>Rhg1</italic>, <italic> Rhg1‐b</italic>, is responsible for protecting most US soybean production from SCN. Whole‐genome sequencing was performed, and PCR assays were developed to investigate allelic variation in sequence and copy number of the <italic>Rhg1</italic> locus across a population of soybean germplasm accessions. Four distinct sequences of the 31.2‐kb repeat unit were identified, and some <italic>Rhg1</italic> alleles carry up to three different types of repeat unit. The total number of copies of the repeat varies from 1 to 10 per haploid genome. Both copy number and sequence of the repeat correlate with the resistance phenotype, and the <italic>Rhg1</italic> locus shows strong signatures of selection. Significant linkage disequilibrium in the genome outside the boundaries of the repeat allowed the <italic>Rhg1</italic> genotype to be inferred using high‐density single nucleotide polymorphism genotyping of 15 996 accessions. Over 860 germplasm accessions were found likely to possess <italic>Rhg1</italic> alleles. The regions surrounding the repeat show indications of non‐neutral evolution and high genetic variability in populations from different geographic locations, but without evidence of fixation of the resistant genotype. A compelling explanation of these results is that balancing selection is in operation at <italic>Rhg1</italic>.</p> </abstract>