《植物生理学报》 2018, 54(6): 1029-1037

基于SLAF-seq技术的木薯SNP标记开发

俞奔驰, 韦丽君^*, 雷开文, 宋恩亮, 马崇熙

广西壮族自治区亚热带作物研究所, 广西南宁530001

通信作者：韦丽君；E-mail: weilijun2002@126.com

摘　要：

开发大量木薯(Manihot esculenta)特异分子标记可促进木薯种质资源中优良基因的挖掘和利用。本研究以39份木薯种质资源为材料, 利用特异性位点扩增片段测序(specific-locus amplified fragment sequencing, SLAF-seq)技术进行测序, 结果显示: 本次实验双端比对效率为90.83%, 酶切效率为91.18%; 通过测序获得304.30 Mb的读长数据, 各样本读长范围在2 123 094~15 102 046之间, 对照数据量最小, 仅395 790个读长; 样品测序质量值(Q₃₀)在95.62%~96.60%之间, 均在95%以上; GC含量在41.27%~44.96%之间, 平均GC含量为42.89%, 对照的GC含量为42.93%。本研究共开发出725 220个SLAF标签, 样本的平均测序深度为20.98倍(×), 多态性SLAF标签446 789个, 共得到2 504 553个群体SNP标记。可见, SLAF-seq技术适用于木薯SNP位点的开发, 其效率较高。

关键词：木薯; 分子标记; SLAF-seq; SNP

收稿：2018-03-20   修定：2018-05-15

资助：广西科技计划项目(桂科AB16380080和桂科AA16380002)和广西自然科学基金(2017GXNSFBA198172)。

Development of SNP markers in cassava (Manihot esculenta Crantz) based on SLAF-seq technology

YU Ben-Chi, WEI Li-Jun^*, LEI Kai-Wen, SONG En-Liang, MA Chong-Xi

Guangxi Subtropical Crops Research Institute, Nanning 530001, China

Corresponding author: WEI Li-Jun; E-mail: weilijun2002@126.com

Abstract:

The development of a large number of specific molecular markers can promote the exploitation and utilization of the excellent genes in cassava (Manihot esculenta Crantz) germplasm resources. Specific-locus amplified fragment sequencing (SLAF-seq) technology was employed to sequence the genomes of 39 cassava varieties/lines in this study. Results show that paired-end alignment efficiency and cleavage efficiency were 90.83% and 91.18%, respectively. 304.30 Mb reads were obtained by sequencing, the reads of the samples varied from 2 123 094 to 15 102 046, and that of the control was the smallest, only 395 790. The sequencing quality value (Q₃₀) changed from 95.62% to 96.60%, all above 95%. The GC content of the samples changed from 41.27% to 44.96%, the average value was 42.89%, and that of the control was 42.93%. Finally, 725 220 SLAF labels were developed, among them 446 789 were polymorphic. The average sequencing depth of the samples was 20.98 ×, and 2 504 553 SNP markers were found. Obviously, SLAF-seq technology is suitable for developing more efficient SNP sites in cassava than ever.

Key words: cassava; molecular marker; SLAF-seq; SNP