Novel Polymorphic Expressed‐Sequence Tag–Simple‐Sequence Repeat Markers in Campeiostachys nutans for Genetic Diversity Analyses

Abstract

ABSTRACTCampeiostachys nutans (Griseb.) J. L. Yang, B. R. Baum et C. Yen is a widely cultivated grass that is used for forage. Considering its limited genomic resources, there is a strong need to increase the available data on this species, which would allow for the identification of genes useful for molecular breeding and lead to increased crop quality and productivity. Complementary DNA (cDNA) samples from 11 different tissues were sequenced using Illumina paired‐end sequencing. A total of 106,220 unigenes were obtained via de novo assembly, and 82,863 (78.01%) unigenes were annotated based on similarity searches using known proteins. In addition, 8727 expressed sequence tag–simple‐sequence repeat (EST‐SSR) loci were identified. A subset of 480 EST‐SSRs was randomly synthesized and screened for validation across a panel of 16 C. nutans accessions using 48 individual plants, with 113 polymorphic EST‐SSRs generating 439 alleles. The number of alleles, observed heterozygosity, expected heterozygosity, and polymorphism information content ranged from three to nine, 0.00 to 1.00, 0.51 to 0.84, and 0.39 to 0.82, respectively. Overall, the C. nutans transcriptomic sequences generated in this study provide both an important platform that will facilitate gene discovery for functional genomic studies and EST‐SSR markers for use in breeding.