生物通报道：张耕耘博士2009年加入深圳华大基因研究院并组建了农业基因组平台，他曾主持或参与了国家自然科学基金、国家“973”等多个大型科研项目，近期他分别以第一作者和通讯作者，在Nature Biotechnology和Nature Genetics杂志上发表文章，取得了谷子和玉米基因组的最新研究进展。

在“Maize HapMap2 identifies extant variation from a genome in flux”这篇文章中，张耕耘博士等人对105个野生和栽培玉米品种进行了测序和分析，成功构建了第二代玉米单体型图谱（简称，Maize HapMap 2），并对玉米的遗传多样性进行了全面分析。

在这篇文章中，研究人员建立了精密的群体遗传学评分模型（population-genetics scoring model），共鉴定了5500多万个遗传分子标记，同时发现染色体结构变异（SV）在玉米野生种和栽培种的基因组中是普遍存在的，并且推测这些结构变异与很多重要的农艺性状具有密切的关联。

此外，在研究影响玉米基因组大小的主要因素时，研究人员发现染色体结（一种密集的DNA结构，chromosomal knobs）的存在或缺失造成了“种内”玉米基因组大小出现很大的差异；而在“种间”进行比较时，他们发现玉米基因组大小的变化则主要与大量的转座子有关。

玉米是集粮、经、饲为一体的三元作物，也是重要的能源作物。遗传多样性研究对玉米种质资源的收集、评价、保存和利用具有十分重要的意义，也对玉米育种具有重要的指导意义。

这项研究与同期另外一项玉米基因组研究对促进玉米改良以满足整个世界对粮食、饲料和燃料等资源的需求具有重要价值。张耕耘博士表示“我们希望在未来的研究中能够取得更多的突破，以便更好地应对全球粮食安全和环境问题所带来的诸多挑战。”

另外一篇“Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential”文章中，研究人员完成了一种植物：谷子（foxtail millet，学名Setaria italica）的全基因组测序，谷是目前种植第二广泛的粟类物种，这项研究为提高谷类粮食遗传性状提供了宝贵的资源。

在这项研究中，研究人员利用新一代测序技术，对一种国内北部谷子品系：张谷（Zhang gu）进行了从头测序（de novo assembly），获得了大小约为423Mb（N50达到了1.0Mb），包含38,801个蛋白编码基因的全基因组序列，这些基因预测超过81%已经表达。通过基因组注释和分析发现，谷子基因组中的重复序列约占整个基因组的46%。

除此之外，研究人员还对另一谷子品系A2进行了重测序——A2是一种广泛使用的谷子杂交雌株品系，利用这两个品系亲本F2代群体，完成了高密度遗传连锁图谱。

（生物通：万纹）

原文摘要：

Maize HapMap2 identifies extant variation from a genome in flux
Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are pervasive in the Z. mays genome and are enriched at loci associated with important traits. By investigating the drivers of genome size variation, we find that the larger Tripsacum genome can be explained by transposable element abundance rather than an allopolyploid origin. In contrast, intraspecies genome size variation seems to be controlled by chromosomal knob content. There is tremendous overlap in key gene content in maize and Tripsacum, suggesting that adaptations from Tripsacum (for example, perennialism and frost and drought tolerance) can likely be integrated into maize.

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

Foxtail millet (Setaria italica), a member of the Poaceae grass family, is an important food and fodder crop in arid regions and has potential for use as a C4 biofuel. It is a model system for other biofuel grasses, including switchgrass and pearl millet. We produced a draft genome (~423 Mb) anchored onto nine chromosomes and annotated 38,801 genes. Key chromosome reshuffling events were detected through collinearity identification between foxtail millet, rice and sorghum including two reshuffling events fusing rice chromosomes 7 and 9, 3 and 10 to foxtail millet chromosomes 2 and 9, respectively, that occurred after the divergence of foxtail millet and rice, and a single reshuffling event fusing rice chromosome 5 and 12 to foxtail millet chromosome 3 that occurred after the divergence of millet and sorghum. Rearrangements in the C4 photosynthesis pathway were also identified.

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