Aegilops tauschii（山羊草） draft genome sequence reveals a gene repertoire for wheat adaptation

Nature

Year published:(2013)

DOI:doi:10.1038/nature12028

Received：28 March 2012

Accepted：20 February 2013

Published online：24 March 2013

 

About 8,000 years ago in the Fertile Crescent（新月）, a spontaneous hybridization of the wild diploid grass Aegilops tauschii (2n = 14; DD) with the cultivated tetraploid wheat Triticum turgidum (2n = 4x = 28; AABB) resulted in hexaploid wheat (T. aestivum; 2n = 6x = 42; AABBDD)^{1, 2}. Wheat has since become a primary staple crop worldwide as a result of its enhanced adaptability to a wide range of climates and improved grain quality for the production of baker’s flour². Here we describe sequencing the Ae. tauschii genome and obtaining a roughly 90-fold depth of short reads from libraries with various insert sizes, to gain a better understanding of this genetically complex plant. The assembled scaffolds represented 83.4% of the genome, of which 65.9% comprised transposable elements. We generated comprehensive RNA-Seq data and used it to identify 43,150 protein-coding genes, of which 30,697 (71.1%) were uniquely anchored to chromosomes with an integrated high-density genetic map. Whole-genome analysis revealed gene family expansion in Ae. tauschii of agronomically relevant gene families that were associated with disease resistance, abiotic stress tolerance and grain quality. This draft genome sequence provides insight into the environmental adaptation of bread wheat and can aid in defining the large and complicated genomes of wheat species.

Affiliations

1. National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China

   • Jizeng Jia,
   • Xiuying Kong,
   • Guangyao Zhao,
   • Xueyong Zhang,
   • Ruilian Jing,
   • Youzhi Ma,
   • Lifeng Gao,
   • Xianchun Xia,
   • Rongzhi Zhang,
   • Xu Liu,
   • Zhonghu He &
   • Long Mao

2. BGI-Shenzhen, Shenzhen 518083, China

   • Shancen Zhao,
   • Yingrui Li,
   • Weiming He,
   • Yong Tao,
   • Chi Zhang,
   • Chuan Gao,
   • Dong Li,
   • Shengkai Pan,
   • Fengya Zheng,
   • Jianwen Li,
   • Qinsi Liang,
   • Jie Chen,
   • Caiyun Gou,
   • Genyun He,
   • Yadan Luo,
   • Qiuju Xia,
   • Peng Lu,
   • Junyi Wang,
   • Hongfeng Zou,
   • Junyang Xu,
   • Jinlong Gao,
   • Zhiwu Quan,
   • Jian Wang,
   • Huanming Yang &
   • Jun Wang

3. State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong

   • Shancen Zhao &
   • Fengya Zheng

4. Centre for Comparative Genomics, Murdoch University, Perth, WA 6150, Australia

   • Rudi Appels

5. MIPS/Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, D-85764 Neuherberg, Germany

   • Matthias Pfeifer,
   • Manuel Spannagl &
   • Klaus F. X. Mayer

6. Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, China

   • Qun Hu &
   • Hanhui Kuang

7. Institute of Plant Biology, University of Zurich, CH-8008 Zurich, Switzerland

   • Thomas Wicker,
   • Beat Keller &
   • Christopher Middleton

8. National Supercomputer Center in Tianjin, Tianjin 300457, China

   • Guangming Liu

9. International Maize and Wheat Improvement Center (CIMMYT), Texcoco CP 56130, Mexico

   • Zhonghu He

10. Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark

    • Jun Wang

11. King Abdulaziz University, Jeddah 21589, Saudi Arabia

    • Jun Wang

Consortia

1. International Wheat Genome Sequencing Consortium

来自：http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12028.html#affil-auth

 

    由中国农业科学院作物科学研究所与深圳华大基因研究院等单位合作，历经5年的努力，在国际上率先完成了小麦D基因组供体种——粗山羊草基因组草图的绘制，结束了小麦没有组装基因组序列的历史（？），标志着我国的小麦基因组研究跨入了世界先进行列。该项成果已于3月24日在线发表在《自然（Nature）》杂志上。
　　据项目牵头人、中国农科院作科所研究员贾继增介绍，小麦D基因组共有7条染色体，约44亿个碱基对，大约是水稻基因组的10倍。通过粗山羊草全基因组分析发现，其抗病相关基因（如NBS-LRR基因等）、抗非生物应激反应的基因数量都发生显著扩张，因而大大增强了其抗病性、抗逆性与适应性。研究发现，在D基因组中有小麦特有的品质相关基因，而且这些也有许多发生了显著扩增，从而使小麦的品质性状大大得到改良，成为唯一能够制作馒头、面包、饺子等多种食品的粮食作物。也正是由于D基因组的加入，才使小麦的抗病性、适应性与品质得到大大改良，推动小麦成为世界上种植区域最广的第一大粮食作物。


　　贾继增对记者说，大量的研究还发现，目前大面积种植的普通小麦的D基因组多样性非常贫乏，已成为制约小麦品种改良的瓶颈。而小麦D基因组的供体种——粗山羊草的遗传多样性非常丰富，其中蕴含着许多优良基因。此次小麦D基因组序列草图的成功绘制，为粗山羊草的开发利用及进一步的品种改良奠定了基础，对小麦育种、小麦种质资源、小麦功能基因组、小麦进化及比较基因组研究将产生巨大的推动作用，有望使小麦常规育种与杂交小麦取得突破性进展。


　　贾继增告诉记者，研究团队今后将围绕小麦基因组的精细图与单倍型图谱构建、小麦种质资源的变异组学与基因发掘等方面与全国有关单位开展协作攻关，有望使我国的小麦研究在未来的5年内跃居世界领先水平，实现我国小麦研究者数百年来的中国梦。


　　据了解，小麦及其祖先种原产于西亚（以色列、伊拉克、伊朗、叙利亚、土耳其等）地区的一个很小的“新月沃”地带，在大约8000-10000年前，小麦的四倍体种（AB基因组）与粗山羊草（D基因组）通过天然杂交，生成了六倍体小麦（ABD基因组），此后才“冲出新月沃，走向世界”，发展成为全世界最主要的粮食作物。


（ 来源：农业部网站 作者：梁宝忠 ）