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首页> 外文期刊>Acta Horticulturae >Towards a Reference Pecan Genome Sequence
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Towards a Reference Pecan Genome Sequence

机译：走向参考山核桃基因组序列

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The cost of generating DNA sequence data has declined dramatically over the previous 15 years as a result of the Human Genome Project and the potential applications of genome sequencing for human medicine. This cost reduction has generated renewed interest among crop breeding scientists in applying sequencing and new genomic tools to accelerate traditional breeding programs by both increasing the specificity of offspring selection and by better understanding the genetic material within a program to reduce breeding cycle times. Pecan (Carya illinoinensis) is an important native tree nut crop with production that averaged over 130 metric tons (t)/y from 2010 to 2012, with farm gate value of over $ 600 million/y (NASS, 2013). Pecan trees have extendedperiods of juvenility before they begin to bear and the time from initial cross to release has averaged almost 30 years for the 29 pecan cultivars released by the USDA ARS Pecan Breeding Program. In order to assess the feasibility of applying genomic technologies to pecan improvement, we generated low-cost, short-read sequences for two pecan cultivars, the commonly planted cultivar 'Pawnee' and a Mexican derived accession named 87MX3-2.il. We assembled these sequences, and assessed genomic repeat content and polymorphism rate between the two haplotypes for each tree. We also identified SNPs and short indels within each of the two cultivars and between the two cultivars based on comparing this short read data to the reference assembly for 87MX3-2.il. Finally, we suggest a path forward for generating a reference pecan genome sequence as a platform for accelerating crop improvement, taking advantage of current genomic technologies.
机译：在过去的15年中，由于人类基因组计划以及人类医学的基因组测序的潜在应用，生成DNA序列数据的成本已大大降低。这种降低成本的方式引起了作物育种科学家的新兴趣，他们希望通过增加后代选择的特异性以及更好地了解减少育种周期时间的计划中的遗传物质，来应用测序和新的基因组工具来加速传统育种计划。山核桃（山核桃illinoinensis）是一种重要的本地树坚果作物，2010年至2012年的平均产量超过130公吨/年，农场的门槛价值超过6亿美元/年（NASS，2013）。美国山核桃树育成计划发布的29种山核桃品种，从开始杂交到释放，山核桃树的存活期已经延长。为了评估将基因组技术应用于山核桃改良的可行性，我们针对两个山核桃品种（通常种植的品种'Pawnee'和墨西哥衍生品名为87MX3-2.il）生成了低成本，短读序列。我们组装了这些序列，并评估了每棵树的两个单倍型之间的基因组重复含量和多态性率。我们还通过将这些短读数据与87MX3-2.il的参考程序集进行了比较，确定了两个品种中以及两个品种之间的SNP和短indel。最后，我们建议利用当前的基因组技术，开发参考山核桃基因组序列作为加速作物改良的平台。

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