Whole Genome Sequencing Reveals the Islands of Novel Polymorphisms in Two Native Aromatic Japonica Rice Landraces from Vietnam.
Whole Genome Sequencing Reveals the Islands of Novel Polymorphisms in Two Native Aromatic Japonica Rice Landraces from Vietnam.
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DOI：
10.1093/gbe/evx135
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发表时间：
2017-06-01
影响因子：
3.3
通讯作者：
Nguyen XH
中科院分区：
文献类型：
--
作者：
Trung KH;Nguyen TK;Khuat HBT;Nguyen TD;Khanh TD;Xuan TD;Nguyen XH
水稻基因组的解析不仅将拓宽我们对农艺性状遗传特征的理解，还将通过标记辅助育种促进水稻的遗传改良。然而，香稻品种的基因组资源在很大程度上尚未被开发利用。因此，对越南北部两个优良的传统粳型香稻地方品种——北宁Tam Xoan（TXBN）和海后Tam Xoan（TXHH）的全基因组进行了测序，以确定它们全基因组的多态性。总体而言，我们在每个香稻地方品种中鉴定出了超过40,000个新的多态性。尽管在两个水稻地方品种中，BADH2基因第7外显子的5 -bp缺失上游都存在一个不连续的8 -bp缺失和一个A/T单核苷酸多态性（SNP），但TXBN的SNP高分辨率区域数量是TXHH的6倍。此外，在两个基因组中都发现了几个新SNP和插入缺失（indel）的热点区域，提供了它们与香气形成相关的潜在基因库。本研究中描述的两个香稻地方品种的基因组信息将有助于香稻相关基因的鉴定以及水稻的遗传改良。
Elucidation of the rice genome will not only broaden our understanding of genetic characterization of the agronomic characteristics but also facilitate the rice genetic improvement through marker assisted breeding. However, the genome resources of aromatic rice varieties are largely unexploited. Therefore, the whole genome of two elite aromatic traditional japonica rice landraces in North Vietnam, Tam Xoan Bac Ninh (TXBN), and Tam Xoan Hai Hau (TXHH), was sequenced to identify their genome-wide polymorphisms. Overall, we identified over 40,000 novel polymorphisms in each aromatic rice landrace. Although a discontinuous 8-bp deletion and an A/T SNP just upstream the 5-bp deletion in exon 7 of BADH2 gene were present in both rice landraces, the number of SNP high resolution regions of TXBN was six times higher than that of TXHH. Furthermore, several hot spot regions of novel SNPs and indels were found in both genomes, providing their potential gene pools related to aroma formation. The genomic information of two aromatic rice landraces described in this study will facilitate the identification of fragrance-related genes and the genetic improvement of rice.
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作者：
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