The genome of cowpea (Vigna unguiculata [L.] Walp.)
Stefano Lonardi,María Muñoz-Amatriaín,Qihua Liang,Shengqiang Shu,Steve Wanamaker,Sassoum Lo,Jaakko Tanskanen,Alan H. Schulman,Tingting Zhu,Ming-Cheng Luo,Hind Alhakami,Rachid Ounit,Abid Hasan,Jerome Verdier,Philip A. Roberts,Jansen R. P. Santos,Jansen R. P. Santos,Arsenio Ndeve,Jaroslav Doležel,Jan Vrána,Samuel Hokin,Andrew Farmer,Steven B. Cannon,Timothy J. Close +23 more
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TLDR
A comparative analysis of elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons, and genes are more abundant in more distal, high‐recombination regions of the chromosomes.Abstract:
Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub-Saharan Africa, that is resilient to hot and drought-prone environments. An assembly of the single-haplotype inbred genome of cowpea IT97K-499-35 was developed by exploiting the synergies between single-molecule real-time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination-poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. Conversely, genes are more abundant in more distal, high-recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS-LRR and the SAUR-like auxin superfamilies compared with other warm-season legumes that have been sequenced. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented.read more
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A receptor-like protein mediates plant immune responses to herbivore-associated molecular patterns.
Adam D. Steinbrenner,Adam D. Steinbrenner,María Muñoz-Amatriaín,María Muñoz-Amatriaín,Antonio F. Chaparro,Jessica Montserrat Aguilar-Venegas,Jessica Montserrat Aguilar-Venegas,Sassoum Lo,Satohiro Okuda,Gaétan Glauser,Julien Dongiovanni,Da Shi,Marlo Hall,Daniel Crubaugh,Nicholas Holton,Cyril Zipfel,Cyril Zipfel,Ruben Abagyan,Ted C. J. Turlings,Timothy J. Close,Alisa Huffaker,Eric A. Schmelz +21 more
TL;DR: The role of plant immune receptors in the perception of chewing herbivores and defense is supported, and a corresponding leucine-rich repeat receptor is identified, specific to select legume species and sufficient to confer inceptin-induced responses and enhanced defense against armyworms in tobacco.
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Genomic resources in plant breeding for sustainable agriculture.
Mahendar Thudi,Ramesh Palakurthi,James C. Schnable,Annapurna Chitikineni,Susanne Dreisigacker,Emma S. Mace,Rakesh K. Srivastava,C. Tara Satyavathi,Damaris A. Odeny,Vijay K. Tiwari,Hon-Ming Lam,Yan Bin Hong,Vikas K. Singh,Guowei Li,Yunbi Xu,Xiaoping Chen,Sanjay Kaila,Henry T. Nguyen,Sobhana Sivasankar,Scott A. Jackson,Timothy J. Close,Wan Shubo,Rajeev K. Varshney +22 more
TL;DR: This review focuses on genomic resources, genome and germplasm sequencing, sequencing-based trait mapping, and genomics-assisted breeding approaches aimed at developing biotic stress resistant, abiotic stress tolerant and high nutrition varieties in six major cereals and six major legumes.
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Development of new genetic resources for faba bean (Vicia faba L.) breeding through the discovery of gene-based SNP markers and the construction of a high-density consensus map
Estefanía Carrillo-Perdomo,A. Vidal,Jonathan Kreplak,H. Duborjal,Magalie Leveugle,Jorge Duarte,C. Desmetz,Chrystel Deulvot,Blandine Raffiot,Pascal Marget,Nadim Tayeh,Jean-Philippe Pichon,Matthieu Falque,Olivier C. Martin,Judith Burstin,Grégoire Aubert +15 more
TL;DR: The genetic tools developed in this work can be used in association mapping, genetic diversity, linkage disequilibrium or comparative genomics and provide a backbone for map-based cloning.
Journal ArticleDOI
A genome-wide association and meta-analysis reveal regions associated with seed size in cowpea [Vigna unguiculata (L.) Walp].
Sassoum Lo,María Muñoz-Amatriaín,María Muñoz-Amatriaín,Samuel Hokin,Ndiaga Cisse,Philip A. Roberts,Andrew Farmer,Shizhong Xu,Timothy J. Close +8 more
TL;DR: The results suggest that a combination of GWAS meta-analysis with synteny comparison in a related plant is an efficient approach to identify candidate gene (s) for complex traits in cowpea.
Journal ArticleDOI
A chromosome‐scale assembly of the black gram (Vigna mungo) genome
Wirulda Pootakham,Wanapinun Nawae,Chaiwat Naktang,Chutima Sonthirod,Thippawan Yoocha,Wasitthee Kongkachana,Duangjai Sangsrakru,Nukoon Jomchai,Sonicha U-thoomporn,Prakit Somta,Kularb Laosatit,Sithichoke Tangphatsornruang +11 more
TL;DR: High‐quality genome assembly along with the genomic variation information from the germplasm provides valuable resources for accelerating the development of elite varieties through marker‐assisted breeding and for future comparative genomics and phylogenetic studies in legume species.
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