Study on Oat SNP Markers Based on Genotyping Technology

doi:10.7668/hbnxb.201751211

Abstract

Abstract: To accelerate marker assisted selection molecular breeding of oat, we had performed genotyping-by-sequencing (GBS) analysis in a group of oat verities with multiple years of drought tolerance characteristics, including 18 low drought tolerance, 13 moderate drought tolerance, 11 high drought tolerance and 12 uncharacterized oat varieties, respectively. GBS libraries were constructed by PstⅠ/MspⅠ double restriction enzymes digestions and subsequently sequenced based on next generation sequencing technology. Using Stacks pipelines, the reduced oats reference genome were annotated and populations SNPs of each sample was identified through Stacks pipeline. The significance was analyzed using PCA, Fisher Test (Hommel package, R script) and Blast. Sequencing results showed that the number of high quality reads in oat individuals ranged from 4 111 218 to 19 019 296. In total, 753 325 references sequences were annotated. By refer to the reference sequences, the populations SNPs were determined for each sample and in total 74 657 SNPs were identified. Based on the populations SNPs, PCA analysis showed that two clusters were formed, one cluster primarily consisted of 14 low drought tolerance germplasm, whereas another one harbors all 11 high drought-tolerance germplasm. Furthermore, comparison between low and high drought tolerance oats showed that in total 2 937 SNPs were significantly and differentially expressed (FDR<0.05). Blasting of 55 SNPs with the most significant difference (FDR<0.001) hosting sequences indicates 14 SNPs might be involved in variant biological pathways including plant hormone signal transduction. This annotated genomic sequences by this study greatly enriched the present available oat genome database. By alignment with the wheat genomic database, the identified 14 SNPs might play an important role of advancing oats molecular breeding. Moreover, it provides a solid technical basis for further large scale screening of oats germplasm.

Key words: Oats, GBS, Drought tolerance, Genotype, SNP

CLC Number:

S512.03
Q78

DONG Yanhui, LIU Longlong, WEN Xin, YU Yufeng, YANG Fang, LIU Genke, CUI Lin, CAO Qiufen, QIN Yongjun. Study on Oat SNP Markers Based on Genotyping Technology[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2019, 34(1): 97-106. doi: 10.7668/hbnxb.201751211.

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