Development and cross-species/genera transferability of microsatellite markers discovered using 454 genome sequencing in chokecherry (Prunus virginiana L.)
Development and cross-species/genera transferability of microsatellite markers discovered using 454 genome sequencing in chokecherry (Prunus virginiana L.)
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DOI：
10.1007/s00299-012-1315-z
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发表时间：
2012-11-01
影响因子：
6.2
通讯作者：
Dai, Wenhao
中科院分区：
文献类型：
--
作者：
Wang, Hongxia;Walla, James A.;Dai, Wenhao
欧樱桃（Prunus virginiana L.）(2n= 4x = 32）具有四倍体的特性和抗X-病性，是一个独特的遗传和抗病研究的李属植物。然而，没有关于chokecherry的遗传和基因组信息。利用Roche 454测序技术对小樱桃的部分基因组进行了测序。共产生了覆盖4.8Mbp的chokecherry基因组的145，094个读段，并组装了15，113个重叠群，其中11，675个重叠群的大小大于100 bp。从11,675个重叠群中筛选出234个SSR位点，共鉴定出481个SSR位点，设计了246对PCR引物。在246个引物中，有212个引物（86.2%）能有效地扩增出樱桃基因组DNA.所有212个可扩增的chokecherry引物用于扩增来自11个其他蔷薇科物种（酸樱桃、甜樱桃、黑樱桃、桃、杏、李、苹果、海棠、梨、juneberry和乌藨子）的基因组DNA。因此，樱桃SSR引物可以在李属物种和其他蔷薇科物种之间转移。结果表明，可扩增的樱桃和其它李属植物的DNA平均扩增率分别为63.2%和58.7%，而可扩增的樱桃和其它蔷薇科植物的DNA平均扩增率为47.2%。使用下一代测序技术产生的随机基因组序列数据来识别微卫星位点似乎是快速和具有成本效益的，特别是对于没有序列信息的物种。这些SSR标记的序列信息和在种间的可传递性，将为李属和其它蔷薇科植物的遗传研究提供有价值的信息。其中212种为樱桃和其它11种蔷薇科植物的混合种。
Chokecherry (Prunus virginiana L.) (2n = 4x = 32) is a unique Prunus species for both genetics and disease-resistance research due to its tetraploid nature and X-disease resistance. However, no genetic and genomic information on chokecherry is available. A partial chokecherry genome was sequenced using Roche 454 sequencing technology. A total of 145,094 reads covering 4.8 Mbp of the chokecherry genome were generated and 15,113 contigs were assembled, of which 11,675 contigs were larger than 100 bp in size. A total of 481 SSR loci were identified from 234 (out of 11,675) contigs and 246 polymerase chain reaction (PCR) primer pairs were designed. Of 246 primers, 212 (86.2 %) effectively produced amplification from the genomic DNA of chokecherry. All 212 amplifiable chokecherry primers were used to amplify genomic DNA from 11 other rosaceous species (sour cherry, sweet cherry, black cherry, peach, apricot, plum, apple, crabapple, pear, juneberry, and raspberry). Thus, chokecherry SSR primers can be transferable across Prunus species and other rosaceous species. An average of 63.2 and 58.7 % of amplifiable chokecherry primers amplified DNA from cherry and other Prunus species, respectively, while 47.2 % of amplifiable chokecherry primers amplified DNA from other rosaceous species. Using random genome sequence data generated from next-generation sequencing technology to identify microsatellite loci appears to be rapid and cost-efficient, particularly for species with no sequence information available. Sequence information and confirmed transferability of the identified chokecherry SSRs among species will be valuable for genetic research in Prunus and other rosaceous species.Key message A total of 246 SSR primers were identified from chokecherry genome sequences. Of which, 212 were confirmed amplifiable both in chokecherry and other 11 other rosaceous species.