Mining SNP/InDel Loci in Three Pistils Wheat Based on Transcriptome Data

doi:10.7668/hbnxb.20192296

Abstract

Abstract: In order to further locate the Pis1 gene, accelerate the molecular marker-assisted breeding of wheat, and obtain the wheat varieties with high quality, high yield and stable yield. Chuanmai 28(CM28) and its three pistils near-isogenic line CM28TP were used as research materials, the three stages of CM28 and CM28TP young spikes(spikelet length 0.2-0.5 cm, 0.5-0.7 cm, 0.7-1.0 cm) perform transcriptome sequencing, then, the GO database was used to classify and analyze the genes where the mutation site was located, and four SNP markers near the Pis1 gene were selected for verification. The results showed that there were 5 310 common SNP/InDel loci in CM28TP and CM28 young spikes at three stages, including 5 024 SNP loci and 286 InDel loci.In SNP sites, the conversion types(63.33%) were more than the transversion types(31.28%), and the ratio of the two types reached 2.02. There were more insert types(152) than deletion types(134) in InDel site. The SNP/InDel locus was most distributed in the A genome, followed by the B genome and the D genome was the least. The GO classification annotation of SNP/InDel genes showed that genes accounted for the highest proportion in biological processes, followed by cell components and molecular functions. The prediction of the impact of the SNP/InDel loci on protein function indicated that 36 mutant loci severely affected protein function, and 1 279 mutant loci moderately affected protein function. Four SNP sites were screened from the location interval of the Pis1 gene for PCR amplification and sequencing verification, and it was found that these four sites were consistent with the results of RNA-seq analysis, which indicated that the SNP/InDel sites excavated were accurate. This study enriched SNP/InDel markers in wheat and laid a foundation for high-density genetic map construction, gene mapping and marker-assisted selection breeding in wheat, at the same time, four SNP markers near the Pis1 gene were developed, which provided the possibility of map-based cloning of this gene.

Key words: Tripistil wheat, Transcriptome, SNP Marker, InDel Marker

CLC Number:

S512.03
Q78

GUO Yuhuan, YAMAMOTO Naoki, PENG Zhengsong, LIAO Mingli, WEI Shuhong, WU Yichao, YANG Zaijun. Mining SNP/InDel Loci in Three Pistils Wheat Based on Transcriptome Data[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2021, 36(5): 35-42. doi: 10.7668/hbnxb.20192296.

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