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园艺学报 ›› 2018, Vol. 45 ›› Issue (8): 1551-1562.doi: 10.16420/j.issn.0513-353x.2018-0301

• 研究论文 • 上一篇    下一篇

基于全基因组序列的马铃薯SSR标记开发与连锁图谱加密

肖桂林1,徐竹清1,曹红菊1,李竟才2,夏军辉1,*,宋波涛1   

  1. 1华中农业大学园艺林学学院,园艺植物生物学教育部重点实验室,农业与农村部马铃薯生物学与生物技术重点实验室,武汉 430070;2黄冈师范学院大别山特色资源开发湖北省协同创新中心,湖北黄冈 438000
  • 出版日期:2018-08-25 发布日期:2018-08-25
  • 基金资助:
    湖北省科技创新重大项目(2016ABA092);国家现代农业产业技术体系建设专项资金项目(CARS-09-P07)

Development of SSR Markers Based on Potato Genome Sequence and Construction of A Higher-density Linkage Map

XIAO Guilin1,XU Zhuqing1,CAO Hongju1,LI Jingcai2,XIA Junhui1,*,and SONG Botao1   

  1. 1College of Horticulture and Forestry Sciences,Huazhong Agricultural University,Key Laboratory of Horticultural Plant Biology,Ministry of Education,Key Laboratory of Potato Biology and Biotechnology,Ministry of Agriculture and Rural Affairs,Wuhan 430070,China;2Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains,Huanggang Normal University,Huanggang,Hubei 438000,China
  • Online:2018-08-25 Published:2018-08-25

摘要: 本研究检索了马铃薯全基因组范围内的SSR序列,并分析了其分布特点。通过开发设计位于目标染色体上的SSR引物,对连锁图谱进行加密和低温糖化抗性QTL定位。结果表明,马铃薯基因组上分布着28 609条SSR序列,平均分布于12条染色体上。其中2碱基、3碱基和4碱基基序SSR序列分别有15 943、11 053和1 613条,富含A或T的SSR数分别占2碱基、3碱基和4碱基基序SSR总数的88.6%、45.0%和26.0%。根据SSR序列两侧保守的侧翼序列,设计了位于5号染色体(chr05)上的SSR引物40对,其中有35对能有效扩增,20对引物的目标片段有多态性,13对引物的32个多态性位点定位到chr05上,将平均标记间距从9.0 cM缩小为1.7 cM,低温糖化抗性QTL的2 LOD置信区间从26.0 cM缩小为4.0 cM;6号染色体(chr06)上新设计SSR引物59对,有54对能有效扩增,25对引物的目标片段有多态性,12对引物的30个多态性位点被定位到chr06上,将平均标记间距从5.5 cM缩小为3.5 cM,低温糖化抗性QTL区间从9.0 cM缩小为3.7 cM。研究结果为抗低温糖化QTL的图位克隆奠定了良好基础,为马铃薯抗低温糖化分子育种提供了辅助标记。

关键词: 马铃薯, SSR, 标记开发, 遗传图谱, QTL

Abstract: In the present research,we identified SSRs in the released potato genome sequence by in silico survey and analyzed their distribution. Using developed SSR primers on target chromosomes,the linkage map was condensed and our interested QTLs were reanalyzed. The results showed that there were 28 609 SSR sequences distributed on 12 potato chromosomes. Among them,the numbers of 2 base,3 base and 4 base motif SSR sequences were 15 943,11 053 and 1 613,respectively. The number of repetitive sequences rich in A or T accounted for 88.6%,45.0% and 26.0% of the total number of SSR sequences with 2 base,3 base and 4 base motif,respectively. According to the conserved flanking sequences on both sides of the SSR sequence,40 pairs of primers on chromosome 5(chr05)were designed,of which 35 pairs can be effectively amplified and 20 pairs were shown polymorphic. As a result,32 polymorphic loci of 13 pairs of primers were located on chr05. Utilization of these makers reduces the average marker interval from 9.0 cM to 1.7 cM and the interval of the cold-induced sweetening resistant QTL from 26.0 cM to 4.0 cM. Besides,59 pairs of primers on chromosome 6(chr06)were designed,of which 54 pairs were clearly amplified and 25 pairs shown polymorphic. As a result,30 polymorphic loci of 12 pairs of primers were located on chr06,which reduces the average marker interval from 5.5 cM to 3.5 cM and the interval of the cold-induced sweetening resistant QTL from 9.0 cM to 3.7 cM. The results have laid a good foundation for mapping the genes controlling cold-induced sweetening resistance,and also provided related markers for molecular breeding of potato.

Key words: potato, SSR;marker development, linkage map, QTL

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