Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement

被引：173

作者：

Wu, Shan ^{[1
]}

Lau, Kin H. ^{[2
]}

Cao, Qinghe ^{[1
,3
]}

Hamilton, John P. ^{[2
]}

Sun, Honghe ^{[1
,4
]}

Zhou, Chenxi ^{[5
]}

Eserman, Lauren ^{[6
,17
]}

Gemenet, Dorcus C. ^{[7
]}

Olukolu, Bode A. ^{[8
,9
]}

Wang, Haiyan ^{[2
,10
]}

Crisovan, Emily ^{[2
]}

Godden, Grant T. ^{[2
]}

Jiao, Chen ^{[1
]}

Wang, Xin ^{[1
]}

Kitavi, Mercy ^{[11
]}

Manrique-Carpintero, Norma ^{[2
]}

Vaillancourt, Brieanne ^{[2
]}

Wiegert-Rininger, Krystle ^{[2
]}

Yang, Xinsun ^{[12
]}

Bao, Kan ^{[1
]}

Schaff, Jennifer ^{[13
]}

Kreuze, Jan ^{[7
]}

Gruneberg, Wolfgang ^{[7
]}

Khan, Awais ^{[7
,18
]}

Ghislain, Marc ^{[11
]}

Ma, Daifu ^{[3
]}

Jiang, Jiming ^{[2
,10
]}

Mwanga, Robert O. M. ^{[14
]}

Leebens-Mack, Jim ^{[6
]}

Coin, Lachlan J. M. ^{[5
]}

Yencho, G. Craig ^{[8
]}

Buell, C. Robin ^{[2
,15
]}

Fei, Zhangjun ^{[1
,16
]}

机构：

[1] Cornell Univ, Boyce Thompson Inst, Ithaca, NY 14853 USA

[2] Michigan State Univ, Dept Plant Biol, E Lansing, MI 48824 USA

[3] Jiangsu Xuzhou Sweetpotato Res Ctr, Xuzhou 221131, Jiangsu, Peoples R China

[4] Beijing Acad Agr & Forestry Sci, Natl Engn Res Ctr Vegetables, Beijing 100097, Peoples R China

[5] Univ Queensland, Inst Mol Biosci, Brisbane, Qld 4072, Australia

[6] Univ Georgia, Dept Plant Biol, Athens, GA 30602 USA

[7] Int Potato Ctr, Lima 12, Peru

[8] North Carolina State Univ, Dept Hort Sci, Raleigh, NC 27695 USA

[9] Univ Tennessee, Dept Entomol & Plant Pathol, Knoxville, TN 37996 USA

[10] Michigan State Univ, Dept Hort, E Lansing, MI 48824 USA

[11] Int Potato Ctr, Nairobi 00603, Kenya

[12] Hubei Acad Agr Sci, Food Crops Inst, Wuhan 430064, Hubei, Peoples R China

[13] North Carolina State Univ, Genom Sci Lab, Raleigh, NC 27695 USA

[14] Int Potato Ctr, Kampala, Uganda

[15] Michigan State Univ, Plant Resilience Inst, E Lansing, MI 48824 USA

[16] ARS, USDA, Robert W Holley Ctr Agr & Hlth, Ithaca, NY 14853 USA

[17] Atlanta Bot Garden, Dept Conservat & Res, Atlanta, GA 30309 USA

[18] Cornell Univ, Plant Pathol & Plant Microbe Biol Sect, Geneva, NY 14456 USA

来源：

NATURE COMMUNICATIONS | 2018年 / 9卷

基金：

中国国家自然科学基金; 美国国家科学基金会; 比尔及梅琳达.盖茨基金会;

关键词：

COPY NUMBER VARIATION; PHYLOGENETIC-RELATIONSHIPS; IPOMOEA-TRIFIDA; INFERENCE; TOOL; TOLERANCE; EVOLUTION; ALIGNMENT; UNCOVERS; POLLEN;

D O I：

10.1038/s41467-018-06983-8

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Sweetpotato [Ipomoea batatas (L.) Lam.] is a globally important staple food crop, especially for sub-Saharan Africa. Agronomic improvement of sweetpotato has lagged behind other major food crops due to a lack of genomic and genetic resources and inherent challenges in breeding a heterozygous, clonally propagated polyploid. Here, we report the genome sequences of its two diploid relatives, I. trifida and I. triloba, and show that these high-quality genome assemblies are robust references for hexaploid sweetpotato. Comparative and phylogenetic analyses reveal insights into the ancient whole-genome triplication history of Ipomoea and evolutionary relationships within the Batatas complex. Using resequencing data from 16 genotypes widely used in African breeding programs, genes and alleles associated with carotenoid biosynthesis in storage roots are identified, which may enable efficient breeding of varieties with high provitamin A content. These resources will facilitate genome-enabled breeding in this important food security crop.

引用

页数：12

共 68 条

[1] INTROGRESSIVE HYBRIDIZATION BETWEEN IPOMOEA-TRICHOCARPA AND IPOMOEA-LACUNOSA (CONVOLVULACEAE) [J].

ABEL, WE ;

AUSTIN, DF .

BULLETIN OF THE TORREY BOTANICAL CLUB, 1981, 108 (02) :231-239

[2]

*AMB GEN PROJ, 2013, SCIENCE, V342, DOI DOI 10.1126/SCIENCE.1241089

[3]

Arumuganathan K., 1991, Plant Mol Biol Rep, V9, P208, DOI [10.1007/BF02672069, DOI 10.1007/BF02672069]

[4]

Austin D.F., 1987, Exploration, Maintenance, Utilization ofSweet Potato Genetic Resources. Proceedings ofthe First Planning Conference, Lima, Peru, P27

[5] MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations [J].

Campbell, Michael S. ;

Law, MeiYee ;

Holt, Carson ;

Stein, Joshua C. ;

Moghe, Gaurav D. ;

Hufnagel, David E. ;

Lei, Jikai ;

Achawanantakun, Rujira ;

Jiao, Dian ;

Lawrence, Carolyn J. ;

Ware, Doreen ;

Shiu, Shin-Han ;

Childs, Kevin L. ;

Sun, Yanni ;

Jiang, Ning ;

Yandell, Mark .

PLANT PHYSIOLOGY, 2014, 164 (02) :513-524

[6] Novel interspecific hybridization between sweetpotato (Ipomoea batatas (L.) Lam.) and its two diploid wild relatives [J].

Cao, Qinghe ;

Zhang, An ;

Ma, Daifu ;

Li, Hongmin ;

Li, Qiang ;

Li, Peng .

EUPHYTICA, 2009, 169 (03) :345-352

[7] Quartet Inference from SNP Data Under the Coalescent Model [J].

Chifman, Julia ;

Kubatko, Laura .

BIOINFORMATICS, 2014, 30 (23) :3317-3324

[8] Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean [J].

Cook, David E. ;

Lee, Tong Geon ;

Guo, Xiaoli ;

Melito, Sara ;

Wang, Kai ;

Bayless, Adam M. ;

Wang, Jianping ;

Hughes, Teresa J. ;

Willis, David K. ;

Clemente, Thomas E. ;

Diers, Brian W. ;

Jiang, Jiming ;

Hudson, Matthew E. ;

Bent, Andrew F. .

SCIENCE, 2012, 338 (6111) :1206-1209

[9] Gene Pool Subdivision of East African Sweetpotato Parental Material [J].

David, Maria C. ;

Diaz, Federico C. ;

Mwanga, Robert O. M. ;

Tumwegamire, Silver ;

Mansilla, Roberto C. ;

Gruneberg, Wolfgang J. .

CROP SCIENCE, 2018, 58 (06) :2302-2314

[10] Phylogeny and substitution rates of angiosperm actin genes [J].

deSa, MM ;

Drouin, G .

MOLECULAR BIOLOGY AND EVOLUTION, 1996, 13 (09) :1198-1212

← 1 2 3 4 5 6 7 →