Genome-wide DNA polymorphisms in four Actinidia arguta genotypes based on whole-genome re-sequencing
Genome-wide DNA polymorphisms in four Actinidia arguta genotypes based on whole-genome re-sequencing
复制标题
基于全基因组重测序的软枣猕猴桃四种基因型的全基因组DNA多态性
DOI：
10.1371/journal.pone.0219884
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发表时间：
2020-04-10
期刊：
影响因子：
3.7
通讯作者：
Zhong, Yunpeng
中科院分区：
文献类型：
--
作者：
Lin, Miaomiao;Fang, Jinbao;Zhong, Yunpeng
Among the genus Actinidia, Actinidia arguta possesses the strongest cold resistance and produces fresh fruit with an intense flavor. To investigate genomic variation that may contribute to variation in phenotypic traits, we performed whole-genome re-sequencing of four A. arguta genotypes originating from different regions in China and identified the polymorphisms using InDel markers. In total, 4,710,650, 4,787,750, 4,646,026, and 4,590,616 SNPs and 1,481,002, 1,534,198, 1,471,304, and 1,425,393 InDels were detected in the 'Ruby-3', 'Yongfeng male', 'Kuilv male', and 'Hongbei male' genomes, respectively, compared with the reference genome sequence of cv 'Hongyang'. A subset of 120 InDels were selected for re-sequencing validation. Additionally, genes related to non-synonymous SNPs and InDels in coding domain sequences were screened for functional analysis. The analysis of GO and KEGG showed that genes involved in cellular responses to water deprivation, sucrose transport, decreased oxygen levels and plant hormone signal transduction were significantly enriched in A. arguta. The results of this study provide insight into the genomic variation of kiwifruit and can inform future research on molecular breeding to improve cold resistance in kiwifruit.
