Development and functional verification of cSSR markers for recessive genetic male sterility in oats

doi:10.11686/cyxb2014232

Abstract

Abstract: The objective of this study was to develop new cSSR markers from an oat (Anena sativa) recessive genes male sterile transcriptome database. EST sequences obtained from a RNA-Seq of oat male sterile near-isogenic line CAMS9 were used to search for SSRs using software. cSSR primers were developed and functional verification for those related to male sterility was determined with a F₂ population of hybridized CAMS9 and Pinyan 2.6409 EST sequences obtained from the transcriptome sequencing had SSR loci and 736 of these sequences had 2 or more loci. Most of the sequence motifs were dinucleotides (56.66%) and trinucleotides (24.30%). For trinucleotides, CCG/CGG (26.68%), AGG/CTT (21.29%), AGC/CTG (18.48%), AAG/CTT (8.18%) and ACC/GGT (8.11%) were the most frequent repeats. For dinucleotides, AG/CT (60.63%) and AC/GT (26.24%) were the most frequent. Based on these cSSRs, 13344 pairs of cSSR primers were designed. 45 pairs of the primers were synthesized based on male sterile-related cSSRs, and 32 (71.1%) of the pairs led to amplified products. Using the F₂ population, the polymorphism of 11 pairs between parents and the differences of 7 pairs between fertile and sterile trait pools were detected. In total, 13344 pairs of cSSR primers have been developed from the RNA-Seq database. 32 pairs were related to fertility and 7 can be used for molecular detection of oat male sterility. These new cSSR markers are beneficial for the further use of oat germplasm and for the study of male sterility.

ZHANG Li-Jun, LIU Long-Long, CHANG Zhi-Jian, GUO Bin, CUI Lin. Development and functional verification of cSSR markers for recessive genetic male sterility in oats[J]. Acta Prataculturae Sinica, 2015, 24(7): 146-154.

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