水稻抗旱QTL区域的连锁不平衡结构
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摘要
本文选取国内外有代表性的籼稻品种和粳稻品种为材料,研究水稻抗旱QTL区域的单核苷酸多态性及连锁不平衡结构,探讨采用关联分析发掘水稻抗旱基因的可行性,主要结果如下：
1.选取来自国内外籼稻品种42份,粳稻品种28份为实验材料,测序获得分布在水稻6条染色体上的6个QTL区域内98个位点总长为46895bp的DNA序列,采用DNASP软件分析发现了455个SNPs,其中转换306个,颠换149个,转换与颠换的比值约为2.05：1,与理论值2：1相当。籼稻中有371个SNPs, SNP频率(θw)为1.84×10-3,π值为1.74×10-3；粳稻中有271个SNPs, SNP频率(θw)为1.49×10-3,π值为0.76×10-3。籼稻和粳稻中都存在丰富的单核苷酸多态性,籼稻大于粳稻。6个QTL区域之间单核苷酸多态性的频率存在较大差异：在籼稻中,QTL QRT10区域最高(θw=2.31×10-3), QTL QRfp12区域的SNPs频率最低(θw=1.15×10-3),相差达两倍。在粳稻中,OA8.1区域上最高(θw=2.70×10-3),QRfp12区域SNPs频率最低(θw=0.48×10-3),相差五倍多。
2.对比籼粳群体的次等位基因频率发现,籼稻和粳稻群体中分布最多的均为次等位基因频率小于等于10%的稀有SNPs位点。粳稻表现得更为明显,在271个SNPs位点中有121个是频率小于等于10%的稀有SNPs位点,占总数的44.6%；而籼稻中,在371个SNPs位点中有131个是频率小于等于10%的稀有SNPs位点,占总数的35.3%。而且在不同的QTL区域,稀有SNPs数目相差较大,籼稻在QTL qDT-5区域稀有SNPs所占的比例最大,为81.1%,在QRfp12区域所占比例最小,仅为6.3%；粳稻在QRT10区域稀有SNPs所占的比例达100%,而在OA8.1区域仅占24.1%。
3.籼粳群体在6个水稻抗旱QTL区域呈现出不同的连锁不平衡结构,粳稻群体LD衰减距离为500-1500kb以上,籼稻群体LD衰减距离为500-1500kb。粳稻连锁不平衡强度R2平均值为0.2957,籼稻R2平均值为0.2473,粳稻的连锁不平衡强度大于籼稻。籼稻R2平均值在QTL PRL11.1最小,为0.0840,在QTL qCC-1最大,为0.3535；粳稻R2平均值在QTL PRL11.1最小,为0.1334,在QTL qDT-5最大,为0.4389,说明同一群体在不同染色体上QTL区域连锁不平衡强度差异较大。
4.基于SNP单倍型进行聚类分析,结果发现籼稻和粳稻明显地聚为两大独立类群,但是无论是在籼稻还是粳稻中,水稻和旱稻的区别并不明显,互相混杂。表明籼稻和粳稻的群体差异高于水稻和旱稻的差异。
5.对抗旱性与SNP/单倍型进行关联分析,发现QTL qCC-1、qDT-5、OA8.1和PRL11.1都与抗旱性之间存在着显著的关联,与抗旱性关联性最强的标记位于11号染色体上PRL11.1 QTL,关联分析与QTL定位结果吻合的比率高达67%,说明用关联分析方法发掘抗旱基因是可能的。
We choose representative Chinese and foreign cultivated rice including accessions of indica and japinica for the study of single nucleotide polymorphisms (SNPs) and linkage disequilibrium (LD), to explore the feasibility of association analysis in finding rice drought-resistant gene. The mainly results are as follows:
1. Ninety eight DNA fragments which distribution on six drought-resistance QTL of Oryza sativa L. were successfully sequenced in 42 Indica and 28 Japonica. The total length of the sequence is 46895 bp.455 single-base changes (SNPs) were found. There were 306 transitions and 149 transversions in all single-base changes (SNPs). And TslTv was 2.05:1, which is consistent with the theoretical ratio 2:1. There are 371 SNPs in Indica, the SNPs frequencies (θw) in indica is 1.84×10-3,πis 1.74×10-3. There are 271 SNPs in japonica, the SNPs frequencies (θw) in japonica is 1.49×10-3,πis 0.76×10-3, the SNPs frequencies in indica are higher than in japonica. The SNPs frequencies in the six QTL region are significantly different. In indica, QTL QRT10 has the highest SNPs frequency (0w=2.31×10-3). QTL QRfp12 has the lowest SNPs frequency (9w=1.15×10-3). In japonica, QTL QRT10 has the highest SNPs frequency (9w=2.70×10-3). QTL QRfp12 has the lowest SNPs frequency (9w=0.48×10-3), a difference of more than five times.
2. The most SNPs have Minor SNPs frequency≤10% in Indica and Japonica. the number of SNPs tends to reduce when the Minor SNPs frequency increase. japonica has more rare SNPs, There are 121 SNPs with Minor SNPs frequency (<10%) in 271 SNPs, the frequency is 44.6%. In indica, there are 131 SNPs with Minor SNPs frequency (<10%) in 371 SNPs. the frequency is 35.3%, The number of rare SNPs is different in different QTL regions. In Indica, the proportion of rare SNPs in QTL qDT-5 is 81.1%, the proportion of rare SNPs in QTL QRfp12 is 6.3%. In Japonica, the proportion of rare SNPs in QTL QRT10 is 100%, the proportion of rare SNPs in QTL OA8.1 is 24.1%.
3. Linkage disequilibrium structures were detected in the six investigated drought-resistance QTL regions. Each regions show different patterns of LD, The extent of LD in japonica group is500->1500 kb, the extentof LD in indica group is 500-1500 kb. The median R2 values of japonica group is 0.2957, indica group is 0.2473. The extent of LD in japonica is larger than indica. In indica, QTL PRL11.1 has the lowest R2 values (0.0840), QTL qCC-1 has the largest R2 values (0.3535). In japonica, QTL PRL11.1 has the lowest R2 values (0.1334), QTL qDT-5 has the largest R2 values (0.4389). It shows that different QTL regions has different LD structure even in the same group.
4. Cluster analysis based on SNPs haplotype shows that indica and japonica clearly clustered into two separate groups, but both in the indica and japonica, the difference of lowland rice and upland rice is not obvious, mixed with each other. It shows that the differences between indica and. japonica are higher than lowland rice and upland rice.
5. The association analysis show that QTL qCC-1, qDT-5, OA8.1, PRL11.1 associated with drought-resistance, and the most notable association was on QTL PRL11.1 of chromosome 11. The ratio of QTL linkage analysis agree with association analysis is 67%, it suggests that association analysis in finding rice drought-resistance genes is possible.
1.选取来自国内外籼稻品种42份,粳稻品种28份为实验材料,测序获得分布在水稻6条染色体上的6个QTL区域内98个位点总长为46895bp的DNA序列,采用DNASP软件分析发现了455个SNPs,其中转换306个,颠换149个,转换与颠换的比值约为2.05：1,与理论值2：1相当。籼稻中有371个SNPs, SNP频率(θw)为1.84×10-3,π值为1.74×10-3；粳稻中有271个SNPs, SNP频率(θw)为1.49×10-3,π值为0.76×10-3。籼稻和粳稻中都存在丰富的单核苷酸多态性,籼稻大于粳稻。6个QTL区域之间单核苷酸多态性的频率存在较大差异：在籼稻中,QTL QRT10区域最高(θw=2.31×10-3), QTL QRfp12区域的SNPs频率最低(θw=1.15×10-3),相差达两倍。在粳稻中,OA8.1区域上最高(θw=2.70×10-3),QRfp12区域SNPs频率最低(θw=0.48×10-3),相差五倍多。
2.对比籼粳群体的次等位基因频率发现,籼稻和粳稻群体中分布最多的均为次等位基因频率小于等于10%的稀有SNPs位点。粳稻表现得更为明显,在271个SNPs位点中有121个是频率小于等于10%的稀有SNPs位点,占总数的44.6%；而籼稻中,在371个SNPs位点中有131个是频率小于等于10%的稀有SNPs位点,占总数的35.3%。而且在不同的QTL区域,稀有SNPs数目相差较大,籼稻在QTL qDT-5区域稀有SNPs所占的比例最大,为81.1%,在QRfp12区域所占比例最小,仅为6.3%；粳稻在QRT10区域稀有SNPs所占的比例达100%,而在OA8.1区域仅占24.1%。
3.籼粳群体在6个水稻抗旱QTL区域呈现出不同的连锁不平衡结构,粳稻群体LD衰减距离为500-1500kb以上,籼稻群体LD衰减距离为500-1500kb。粳稻连锁不平衡强度R2平均值为0.2957,籼稻R2平均值为0.2473,粳稻的连锁不平衡强度大于籼稻。籼稻R2平均值在QTL PRL11.1最小,为0.0840,在QTL qCC-1最大,为0.3535；粳稻R2平均值在QTL PRL11.1最小,为0.1334,在QTL qDT-5最大,为0.4389,说明同一群体在不同染色体上QTL区域连锁不平衡强度差异较大。
4.基于SNP单倍型进行聚类分析,结果发现籼稻和粳稻明显地聚为两大独立类群,但是无论是在籼稻还是粳稻中,水稻和旱稻的区别并不明显,互相混杂。表明籼稻和粳稻的群体差异高于水稻和旱稻的差异。
5.对抗旱性与SNP/单倍型进行关联分析,发现QTL qCC-1、qDT-5、OA8.1和PRL11.1都与抗旱性之间存在着显著的关联,与抗旱性关联性最强的标记位于11号染色体上PRL11.1 QTL,关联分析与QTL定位结果吻合的比率高达67%,说明用关联分析方法发掘抗旱基因是可能的。
We choose representative Chinese and foreign cultivated rice including accessions of indica and japinica for the study of single nucleotide polymorphisms (SNPs) and linkage disequilibrium (LD), to explore the feasibility of association analysis in finding rice drought-resistant gene. The mainly results are as follows:
1. Ninety eight DNA fragments which distribution on six drought-resistance QTL of Oryza sativa L. were successfully sequenced in 42 Indica and 28 Japonica. The total length of the sequence is 46895 bp.455 single-base changes (SNPs) were found. There were 306 transitions and 149 transversions in all single-base changes (SNPs). And TslTv was 2.05:1, which is consistent with the theoretical ratio 2:1. There are 371 SNPs in Indica, the SNPs frequencies (θw) in indica is 1.84×10-3,πis 1.74×10-3. There are 271 SNPs in japonica, the SNPs frequencies (θw) in japonica is 1.49×10-3,πis 0.76×10-3, the SNPs frequencies in indica are higher than in japonica. The SNPs frequencies in the six QTL region are significantly different. In indica, QTL QRT10 has the highest SNPs frequency (0w=2.31×10-3). QTL QRfp12 has the lowest SNPs frequency (9w=1.15×10-3). In japonica, QTL QRT10 has the highest SNPs frequency (9w=2.70×10-3). QTL QRfp12 has the lowest SNPs frequency (9w=0.48×10-3), a difference of more than five times.
2. The most SNPs have Minor SNPs frequency≤10% in Indica and Japonica. the number of SNPs tends to reduce when the Minor SNPs frequency increase. japonica has more rare SNPs, There are 121 SNPs with Minor SNPs frequency (<10%) in 271 SNPs, the frequency is 44.6%. In indica, there are 131 SNPs with Minor SNPs frequency (<10%) in 371 SNPs. the frequency is 35.3%, The number of rare SNPs is different in different QTL regions. In Indica, the proportion of rare SNPs in QTL qDT-5 is 81.1%, the proportion of rare SNPs in QTL QRfp12 is 6.3%. In Japonica, the proportion of rare SNPs in QTL QRT10 is 100%, the proportion of rare SNPs in QTL OA8.1 is 24.1%.
3. Linkage disequilibrium structures were detected in the six investigated drought-resistance QTL regions. Each regions show different patterns of LD, The extent of LD in japonica group is500->1500 kb, the extentof LD in indica group is 500-1500 kb. The median R2 values of japonica group is 0.2957, indica group is 0.2473. The extent of LD in japonica is larger than indica. In indica, QTL PRL11.1 has the lowest R2 values (0.0840), QTL qCC-1 has the largest R2 values (0.3535). In japonica, QTL PRL11.1 has the lowest R2 values (0.1334), QTL qDT-5 has the largest R2 values (0.4389). It shows that different QTL regions has different LD structure even in the same group.
4. Cluster analysis based on SNPs haplotype shows that indica and japonica clearly clustered into two separate groups, but both in the indica and japonica, the difference of lowland rice and upland rice is not obvious, mixed with each other. It shows that the differences between indica and. japonica are higher than lowland rice and upland rice.
5. The association analysis show that QTL qCC-1, qDT-5, OA8.1, PRL11.1 associated with drought-resistance, and the most notable association was on QTL PRL11.1 of chromosome 11. The ratio of QTL linkage analysis agree with association analysis is 67%, it suggests that association analysis in finding rice drought-resistance genes is possible.
引文
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