高梁基因组内大片段获得与缺失变异挖掘及其与重要农艺性状的关联分析
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摘要
获得与缺失变异（PAVs，presence/absence variants）是一种通过缺失和插入引起的基因组结构变异，直接影响到基因组大小和基因数目变化，带来的基因组变异的尺度远远大于单核苷酸多态性（SNP，single nucleotide polymorphism）或小片段缺失（InDels，insertions and deletions，一般小于10bp）。PAVs广泛存在于人类及动物基因组，对人类多种遗传疾病及动物表型变异起到关键作用。在植物基因组中，已经挖掘出大量PAVs，但对它的起源，形成机理，功能和分子育种利用等研究较少。
高粱（Sorghum bicolour）是一种重要的粮食、经济、能源等多功能C4作物，光合作用效率高，生物产量和经济产量大，同时高粱具有很强的抗逆性和适应性，适合我国中低产田的开发与利用。为满足国家能源和粮食安全需求，我们应该发掘新的基因资源和育种思路加速高粱分子育种进程。本研究利用遗传多样性丰富的高粱自交系，分析高粱基因组中大片段获得与缺失变异（lsPAVs，larger-size presence/absence variants）的类别、数目、分布和遗传多样性；并对关键的lsPAVs进行重要农艺性状的关联分析，建立PAVs-性状关系，解决高粱分子遗传育种基因及重要功能变异位点等资源缺乏的问题。
本实验室已经对三个高粱品种（Keller，E-tian和Ji2731）进行了重测序的工作（每个品种12×数据量），通过比较基因组学分析，在高粱基因组中挖掘出5364个PAVs，其中大于30kb的PAVs有96个，影响了约5.2Mb基因组序列，约占总PAVs影响基因组序列的1/4。通过分子生物学及遗传学方法验证，确定51个大于30kb的lsPAVs在高粱基因组上是以简单插入缺失变异存在，覆盖了约2.92Mb的基因组序列。通过PAVs影响的基因密度分析，发现lsPAVs发生在常染色体低基因密度区域。51个lsPAVs影响了202个已知或预测的基因，包括38个基因响应细胞死亡及生物胁迫，及56个编码转座子表达蛋白的基因。通过RepeatMasker分析，发现lsPAVs序列中包含大量的反转录转座元件和DNA转座子的重复序列以及其他简单重复序列和低复杂度序列。另外，通过BreakSeq分析发现，51个lsPAVs中50个lsPAVs是通过非同源重组（NHR，non-homologousrecombination）导致，仅有一个变异通过非等位基因同源重组（NAHR，non-allelichomologous recombination）形成。基因组间lsPAVs在自然的选择压力下存在着广泛的遗传多样性，分析51个lsPAVs在高粱96自然品种中的分布频率，发现51个lsPAVs在自然群体中分布频率存在很大差异，这种现象与lsPAV影响的基因功能相关，与其序列特征关系不大。根据lsPAVs在高粱遗传分离群体上的分析，发现lsPAVs存在着动态进化过程。通过关联分析手段，发现21个lsPAVs与15个重要农艺性状相关，共挖掘出41个位点，其中有10个lsPAVs影响多个性状，反之发现有10个性状存在关联显著的多态性位点，另外发现其中有23个lsPAVs位点与已经报道的QTLs位点基本一致。
本研究首次对高粱基因组内大片段获得与缺失变异（lsPAVs）的发生，分布，遗传多样性及功能进行了研究，并对lsPAVs进行重要农艺性状的关联分析，建立lsPAVs-性状关系。本研究从新的角度解决甜高粱分子育种的瓶颈，为高粱及相关作物育种提供新手段，为植物功能基因组学研究提供理论参考。
Background
The presence/absence variants (PAVs) are a major source of genome structurevariation and have profound effects on human diseases as well as on genome sizesand phenotypic variation in animals. Little is understood about PAVs in plantgenomes. Sorghum (Sorghum bicolour) is a multi-functional C4crop providing food,feed, fibre and fuel, particularly in low-input water-limiting agriculture systems.Here we report our effort to dissect PAVs’ occurrence, diversity and associationswith biofuel-associated traits in sorghum.
Results
Three sorghum genomes were resequenced to12×coverage each and5364PAVswere uncovered, only including96lsPAVs (large-size PAVs)(larger than30kilobases) which affected5.2Mb genomic sequences. The lsPAVs were studied andthe occurrence of51large-size PAVs was confirmed as simple insertion and deletionevents. These lsPAVs affected a total size of2.92Mb of the sorghum genomecontaining202known and predicted genes, of which38were annotated to encodecell death and stress response genes. Detailed analysis of the genomic sequenceswithin and surrounding the lsPAVs demonstrated that there existed56expressedtransposon proteins and high numbers of repeats sequences of various retroelements,DNA transposons, simple repeats and low complexity sequences, suggesting that thelsPAVs resulted from transposable activities and non-homologous recombination.The frequency and distribution of these PAVs varied substantially in a panel of96sorghum inbred lines, and the low-and high-frequency lsPAVs differed in their gene categories. Our further association analysis demonstrated that21lsPAVs weresignificantly associated with the variation in15agronomic traits,10of the lsPAVsaffected more than one traits and more than half of the identified loci localised inprevious mapped QTLs intervals.
Conclusions
This report, for the first time, shed new lights on the occurrence, diversity andfunctions of lsPAVs in sorghum genomes, and established lsPAVs-trait associations.Our research exemplifies a new perspective to explore genome structure variation forgenetic improvement in plant breeding.
高粱（Sorghum bicolour）是一种重要的粮食、经济、能源等多功能C4作物，光合作用效率高，生物产量和经济产量大，同时高粱具有很强的抗逆性和适应性，适合我国中低产田的开发与利用。为满足国家能源和粮食安全需求，我们应该发掘新的基因资源和育种思路加速高粱分子育种进程。本研究利用遗传多样性丰富的高粱自交系，分析高粱基因组中大片段获得与缺失变异（lsPAVs，larger-size presence/absence variants）的类别、数目、分布和遗传多样性；并对关键的lsPAVs进行重要农艺性状的关联分析，建立PAVs-性状关系，解决高粱分子遗传育种基因及重要功能变异位点等资源缺乏的问题。
本实验室已经对三个高粱品种（Keller，E-tian和Ji2731）进行了重测序的工作（每个品种12×数据量），通过比较基因组学分析，在高粱基因组中挖掘出5364个PAVs，其中大于30kb的PAVs有96个，影响了约5.2Mb基因组序列，约占总PAVs影响基因组序列的1/4。通过分子生物学及遗传学方法验证，确定51个大于30kb的lsPAVs在高粱基因组上是以简单插入缺失变异存在，覆盖了约2.92Mb的基因组序列。通过PAVs影响的基因密度分析，发现lsPAVs发生在常染色体低基因密度区域。51个lsPAVs影响了202个已知或预测的基因，包括38个基因响应细胞死亡及生物胁迫，及56个编码转座子表达蛋白的基因。通过RepeatMasker分析，发现lsPAVs序列中包含大量的反转录转座元件和DNA转座子的重复序列以及其他简单重复序列和低复杂度序列。另外，通过BreakSeq分析发现，51个lsPAVs中50个lsPAVs是通过非同源重组（NHR，non-homologousrecombination）导致，仅有一个变异通过非等位基因同源重组（NAHR，non-allelichomologous recombination）形成。基因组间lsPAVs在自然的选择压力下存在着广泛的遗传多样性，分析51个lsPAVs在高粱96自然品种中的分布频率，发现51个lsPAVs在自然群体中分布频率存在很大差异，这种现象与lsPAV影响的基因功能相关，与其序列特征关系不大。根据lsPAVs在高粱遗传分离群体上的分析，发现lsPAVs存在着动态进化过程。通过关联分析手段，发现21个lsPAVs与15个重要农艺性状相关，共挖掘出41个位点，其中有10个lsPAVs影响多个性状，反之发现有10个性状存在关联显著的多态性位点，另外发现其中有23个lsPAVs位点与已经报道的QTLs位点基本一致。
本研究首次对高粱基因组内大片段获得与缺失变异（lsPAVs）的发生，分布，遗传多样性及功能进行了研究，并对lsPAVs进行重要农艺性状的关联分析，建立lsPAVs-性状关系。本研究从新的角度解决甜高粱分子育种的瓶颈，为高粱及相关作物育种提供新手段，为植物功能基因组学研究提供理论参考。
Background
The presence/absence variants (PAVs) are a major source of genome structurevariation and have profound effects on human diseases as well as on genome sizesand phenotypic variation in animals. Little is understood about PAVs in plantgenomes. Sorghum (Sorghum bicolour) is a multi-functional C4crop providing food,feed, fibre and fuel, particularly in low-input water-limiting agriculture systems.Here we report our effort to dissect PAVs’ occurrence, diversity and associationswith biofuel-associated traits in sorghum.
Results
Three sorghum genomes were resequenced to12×coverage each and5364PAVswere uncovered, only including96lsPAVs (large-size PAVs)(larger than30kilobases) which affected5.2Mb genomic sequences. The lsPAVs were studied andthe occurrence of51large-size PAVs was confirmed as simple insertion and deletionevents. These lsPAVs affected a total size of2.92Mb of the sorghum genomecontaining202known and predicted genes, of which38were annotated to encodecell death and stress response genes. Detailed analysis of the genomic sequenceswithin and surrounding the lsPAVs demonstrated that there existed56expressedtransposon proteins and high numbers of repeats sequences of various retroelements,DNA transposons, simple repeats and low complexity sequences, suggesting that thelsPAVs resulted from transposable activities and non-homologous recombination.The frequency and distribution of these PAVs varied substantially in a panel of96sorghum inbred lines, and the low-and high-frequency lsPAVs differed in their gene categories. Our further association analysis demonstrated that21lsPAVs weresignificantly associated with the variation in15agronomic traits,10of the lsPAVsaffected more than one traits and more than half of the identified loci localised inprevious mapped QTLs intervals.
Conclusions
This report, for the first time, shed new lights on the occurrence, diversity andfunctions of lsPAVs in sorghum genomes, and established lsPAVs-trait associations.Our research exemplifies a new perspective to explore genome structure variation forgenetic improvement in plant breeding.
引文
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