摘要
为了探究怀玉山高山马铃薯只限于高海拔生境下的适应机制,本研究以高海拔生境下怀玉山高山马铃薯和怀玉山本土农家薯采后块茎萌发的芽为材料,进行了全基因组重测序分析。结果表明:HAP的总SNP数量为2 835 211,SNP的密度为3.925 212,编码区nsSNP总数为104 456;LAP的总SNP数量为3 968 618,SNP的密度为5.427 855,编码区nsSNP总数为141 060。经CV分析后,LAP和HAP共有319个nsSNP关联了315个基因,其中76个基因具有超过1个的nsSNP。nsSNP的防御反应、蛋白氨基酸磷酸化、蛋白激酶等GOterms显著富集。HAP的总Indel数量为159 797,编码区的Indel数量为1 850;LAP的总Indel数量为154 291,编码区的Indel数量为1 714;两组的总Indel数量远远小于两组的总SNP数。经差异分析后,共有1 629个Indel关联到了726个基因。Indel的防御反应、胁迫应答、细胞凋亡等GOterms显著富集。nsSNP和Indel的GOterms大多与高海拔生境和光合作用相关。nsSNP和Indel分布在端粒附近相对于中心粒具有更高密度的变异。LAP和HAP共获得了1 490个CNV,其中缺失(Deletion)为610个,中性(Neutral)为548个,扩增(Amplification)为332个。本研究结果可为高海拔生境下怀玉山高山马铃薯的SNP和Indel相关标记的开发、优异基因的挖掘提供重要理论依据。
To explore the adaptation mechanism of alpine potato in Huaiyushan to high altitude habitats, buds generated from postharvest tuber of alpine potato and local farm potato in Huaiyushan under high altitude habitats were analyzed by whole genome sequencing in this study. The results showed that the total SNP number of HAP was 2 835 211, the density of SNP was 3.925 212, the total number of nsSNP in coding area was 104 456;the total SNP number of LAP was 3 968 618, the density of SNP was 5.427 855, the total number of nsSNP in coding area was 141 060. After CV analysis, there were 319 nsSNP between LAP and HAP associated with 315 genes, of which 76 had more than 1 nsSNP. The defense reaction, protein amino acid phosphorylation, protein kinase and other GOterms of nsSNP were significantly enriched. The total number of Indel in HAP was 159 797, the number of Indel in coding area was 185;the total number of Indel in LAP was 154 291, the number of Indel in coding area was 1 714. The total Indel number of two groups was far less than the total SNP number of two groups. After differential analysis, a total of 1 629 indel were associated with 726 genes. GO terms of inde was significantly enriched in l defense response, stress response, cell apoptosis and so on. Most of the GOterms of nsSNP and indel was associated with high altitude habitats and photosynthesis. The distribution of nsSNP and indel in the vicinity of telomere had a higher density variation than that of the central grain. LAP and HAP obtained 1 490 CNV, of which610 were deletion, 548 were neutral, and 332 were amplification. The experimental results provide important reference for development for SNP and Indel markers and mining for excellent genes of alpine potato in Huaiyushanunder high altitude habitats.
作者
尹明华
王钦
张红蕾
蔡晓华
徐呈琦
陈芳丽
刘舒雅
张启薇
蔡红
陈荣华
Yin Minghua;Wang Qin;Zhang Honglei;Cai Xiaohua;Xu Chengqi;Chen Fangli;Liu Shuya;Zhang Qiwei;Cai Hong;Chen Ronghua(College of Life Sciences,Shangrao Normal University,Shangrao,334001;Shangrao Red Sun Agricultural Development Co.,Ltd.,Shangrao,334700)
出处
《基因组学与应用生物学》
CAS
CSCD
北大核心
2020年第3期1198-1207,共10页
Genomics and Applied Biology
基金
国家自然科学基金项目(31860084)资助。
关键词
高海拔生境
怀玉山高山马铃薯
怀玉山本土农家薯
块茎萌发芽
全基因组重测序分析
High altitude habitats
Alpine potato in Huaiyushan
Local farm potato in Huaiyushan
Buds generated from tuber
Whole genome re-sequencing analysis
