Accessing Diversity in Rye (Secale cereale L.) and Its Potential for Crop Improvement.

ABSTRACT:

Rye (Secale cereale L.) is known for its hardiness because it can tolerate harsh winters and can be grown in semiarid areas. Along with its resilience to abiotic stresses, it possess many disease resistance genes, a few of which have been explored for genetic improvement of wheat. To better assess the diversity in rye and utilize it for wheat improvement we selected 180 geographically diverse accessions of Secale sp. from U.S. National Small Grains Collection. All accessions were genotyped by GBS and SNPs were discovered using a reference-based pipeline. We used 747 polymorphic SNPs with less than 30% missing data for genetic diversity analysis and development of a core set. The NJ tree showed two major clusters separating S. cereale L. from S. strictum and S. sylvestre. A core set of 35 accessions was selected, which represents ~97% of the allelic diversity of the collection. Furthermore, the core set has a higher Shanon and Weaver diversity index (I) and Nei’s genetic diversity index (h) (I = 0.43, h = 0.54) as compared to the entire set (I = 0.36, h = 0.48). Our results suggests exploiting genetic diversity would be more useful than random selection and enhance the potential of the germplasm in crop improvement. We further utilized the collection for mapping genes/QTLs conferring resistance to tan spot race 5 by association analysis using GAPIT algorithm. Nearly 33%, 27%, 24%, 16% accessions showed resistant, moderately resistant, moderately susceptible and susceptible reaction to Pyrenophora tritici-repentis. We found two potential genomic regions on chromosome 6R and 2R significantly linked to resistance to tan spot race 5.