基于基因分型技术的燕麦SNP标记研究
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摘要
为加快燕麦分子辅助育种进程,以1981-1983年进行抗旱性鉴定的42份燕麦种质(18份低抗、13份中抗、11份高抗)和12个未鉴定的燕麦育成品种为试验材料,采用PstⅠ/MspⅠ双酶切的dd-GBS基因分型技术构建燕麦简化基因组参考序列,通过Stacks、主成分分析、Fisher Test和Blast分析研究燕麦SNP分子标记。测序结果表明,燕麦个体的高质量reads数在4 111 218～19 019 296,利用Stacks软件成功组装753 325条燕麦简化基因组参考序列,共注释74 657个群体SNP位点。主成分分析表明,燕麦SNP基因型大致聚为2簇,其中一簇主要由14份低抗种质组成,另一簇则包含全部11份高抗种质。进一步的Fisher Test差异显著性统计分析表明,相对于燕麦低抗种质材料,共有2 937个SNP标记在燕麦高抗种质材料中差异显著((错误发现率False Discovery Rate,FDR)<0. 05),其中,55个SNP标记差异极显著(FDR <0. 001)。将上述55个SNP标记所在源序列与小麦基因组序列在Phytozome数据库中进行比对(Blast)发现,14个SNP位点可能参与燕麦抗旱生物学信号通路基因的表达,其中包括参与植物激素信号转导来调控燕麦的抗逆性。通过GBS技术成功组装的燕麦简化基因组参考序列,丰富了当前燕麦的基因组数据库。通过统计学分析得到的55个SNP标记与小麦基因组数据库进行比对,结果发现,14个SNP标记将对燕麦分子辅助育种和加速育种进程具有重要的指导意义,更可为今后的燕麦种质资源大规模快速筛选奠定技术基础。
To accelerate marker assisted selection molecular breeding of oat,we had performed genotyping-bysequencing( GBS) analysis in a group of oat verities with multiple years of drought tolerance characteristics,including 18 low drought tolerance,13 moderate drought tolerance,11 high drought tolerance and 12 uncharacterized oat varieties,respectively. GBS libraries were constructed by PstⅠ/Msp Ⅰ double restriction enzymes digestions and subsequently sequenced based on next generation sequencing technology. Using Stacks pipelines,the reduced oats reference genome were annotated and populations SNPs of each sample was identified through Stacks pipeline.The significance was analyzed using PCA,Fisher Test( Hommel package,R script) and Blast. Sequencing results showed that the number of high quality reads in oat individuals ranged from 4 111 218 to 19 019 296. In total,753325 references sequences were annotated. By refer to the reference sequences,the populations SNPs were determined for each sample and in total 74 657 SNPs were identified. Based on the populations SNPs,PCA analysis showed that two clusters were formed,one cluster primarily consisted of 14 low drought tolerance germplasm,whereas another one harbors all 11 high drought-tolerance germplasm. Furthermore,comparison between low and high drought tolerance oats showed that in total 2 937 SNPs were significantly and differentially expressed( FDR <0. 05). Blasting of 55 SNPs with the most significant difference( FDR < 0. 001) hosting sequences indicates 14 SNPs might be involved in variant biological pathways including plant hormone signal transduction. This annotated genomic sequences by this study greatly enriched the present available oat genome database. By alignment with the wheat genomic database,the identified 14 SNPs might play an important role of advancing oats molecular breeding.Moreover,it provides a solid technical basis for further large scale screening of oats germplasm.
To accelerate marker assisted selection molecular breeding of oat,we had performed genotyping-bysequencing( GBS) analysis in a group of oat verities with multiple years of drought tolerance characteristics,including 18 low drought tolerance,13 moderate drought tolerance,11 high drought tolerance and 12 uncharacterized oat varieties,respectively. GBS libraries were constructed by PstⅠ/Msp Ⅰ double restriction enzymes digestions and subsequently sequenced based on next generation sequencing technology. Using Stacks pipelines,the reduced oats reference genome were annotated and populations SNPs of each sample was identified through Stacks pipeline.The significance was analyzed using PCA,Fisher Test( Hommel package,R script) and Blast. Sequencing results showed that the number of high quality reads in oat individuals ranged from 4 111 218 to 19 019 296. In total,753325 references sequences were annotated. By refer to the reference sequences,the populations SNPs were determined for each sample and in total 74 657 SNPs were identified. Based on the populations SNPs,PCA analysis showed that two clusters were formed,one cluster primarily consisted of 14 low drought tolerance germplasm,whereas another one harbors all 11 high drought-tolerance germplasm. Furthermore,comparison between low and high drought tolerance oats showed that in total 2 937 SNPs were significantly and differentially expressed( FDR <0. 05). Blasting of 55 SNPs with the most significant difference( FDR < 0. 001) hosting sequences indicates 14 SNPs might be involved in variant biological pathways including plant hormone signal transduction. This annotated genomic sequences by this study greatly enriched the present available oat genome database. By alignment with the wheat genomic database,the identified 14 SNPs might play an important role of advancing oats molecular breeding.Moreover,it provides a solid technical basis for further large scale screening of oats germplasm.
引文
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