Rural Development Administration, Genomics Division, National Academy of Agricultural Science, Suwon, 441-707, Republic of Korea.
Rice (N Y). 2013 Mar 14;6(1):6. doi: 10.1186/1939-8433-6-6.
Anther culture has advantage to obtain a homozygous progeny by induced doubling of haploid chromosomes and to improve selection efficiency for invaluable agronomical traits. Therefore, anther culturing is widely utilized to breed new varieties and to induce genetic variations in several crops including rice. Genome sequencing technologies allow the detection of a massive number of DNA polymorphism such as SNPs and Indels between closely related cultivars. These DNA polymorphisms permit the rapid identification of genetic diversity among cultivars and genomic locations of heritable traits. To estimate sequence diversity derived from anther culturing, we performed whole-genome resequencing of five Korean rice accessions, including three anther culture lines (BLB, HY-04 and HY-08), their progenitor cultivar (Hwayeong), and an additional japonica cultivar (Dongjin).
A total of 1,165 × 106 raw reads were generated with over 58× coverage that detected 1,154,063 DNA polymorphisms between the Korean rice accessions and Nipponbare. We observed that in Hwayeong and its progenies, 0.64 SNP was found per one kb of Nipponbare genome, while Dongjin, bred by a conventional breeding method, had a lower number of SNPs (0.45 SNP/kb). Among 1,154,063 DNA polymorphisms, 29,269 non-synonymous SNPs located on 30,013 genes and these genes were functionally classified based on gene ontology (GO). We also analyzed line-specific SNPs which were estimated 1 ~ 3% of the total SNPs. The frequency of non-synonymous SNPs in each accession ranged from 26 SNPs in Hwayeong to 214 SNPs in HY-04.
The genetic difference we detected between the progenies derived from anther culture and their mother cultivar is due to somaclonal variation during tissue culture process, such as karyotype change, chromosome rearrangement, gene amplification and deletion, transposable element, and DNA methylation. Detection of genome-wide DNA polymorphisms by high-throughput sequencer enabled to identify sequence diversity derived from anther culturing and genomic locations of heritable traits. Furthermore, it will provide an invaluable resource to identify molecular markers and genes associated with diverse traits of agronomical importance.
花药培养通过诱导单倍体染色体加倍获得纯合后代，提高了对无价农艺性状的选择效率，具有优势。因此，花药培养被广泛用于培育新品种和诱导包括水稻在内的几种作物的遗传变异。基因组测序技术允许检测到大量 DNA 多态性，如紧密相关品种之间的 SNPs 和 Indels。这些 DNA 多态性允许快速鉴定品种之间的遗传多样性和可遗传性状的基因组位置。为了估计花药培养产生的序列多样性，我们对包括三个花药培养系（BLB、HY-04 和 HY-08）在内的五个韩国水稻品种进行了全基因组重测序，其祖代品种（Hwayeong）和一个附加的粳稻品种（Dongjin）。
共生成了 1165×106 个原始读数，覆盖率超过 58×，在韩国水稻品种和 Nipponbare 之间检测到 1154063 个 DNA 多态性。我们观察到，在 Hwayeong 和其后代中，每 1kb 的 Nipponbare 基因组中发现 0.64 个 SNP，而通过常规育种方法培育的 Dongjin 的 SNP 数量较少（0.45 SNP/kb）。在 1154063 个 DNA 多态性中，29269 个非同义 SNP 位于 30013 个基因上，这些基因根据基因本体论（GO）进行了功能分类。我们还分析了特定于系的 SNP，估计占总 SNP 的 1%~3%。每个品种的非同义 SNP 频率范围从 Hwayeong 的 26 个到 HY-04 的 214 个。
我们在花药培养后代与其母本品种之间检测到的遗传差异是由于组织培养过程中的体细胞变异引起的，如核型变化、染色体重排、基因扩增和缺失、转座子和 DNA 甲基化。高通量测序仪检测全基因组 DNA 多态性能够鉴定来自花药培养的序列多样性和可遗传性状的基因组位置。此外，它将为鉴定与农艺重要性状相关的分子标记和基因提供宝贵资源。
