The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color

Genome Biology

David N Kuhn^1,15  Laxmi Parida⁹  Don Gilbert^1,12  Dorrie Main^1,14  Raymond J Schnell^1,15  Carlos D Bustamante¹  Jianxin Ma^1,13  Howard Shapiro⁶  Gregory D May²  Jean Philippe Marelli³  Wilbert Phillips⁷  Freddy Amores^1,10  Guiliana M Mustiga⁶  Frank A Feltus^1,11  Joseph C Stack⁶  Brian E Scheffler⁸  Meixia Zhao^1,13  Ram Podicheti⁵  Jerry Jenkins⁴  Christopher Saski^1,11  Stefan Royaert^1,15  Filippo Utro⁹  Ping Zheng^1,14  Seth D Findley⁶  Omar Cornejo¹  Donald Livingstone III^1,15  Niina Haiminen⁹  Jeremy Schmutz⁴  Keithanne Mockaitis^1,12  Juan C Motamayor⁶ 

[1] Department of Genetics, Stanford University, 300 Pasteur Dr, Stanford, CA, 94305, USA;National Center for Genome Resources, 2935 Rodeo Park Drive E, Santa Fe, NM, 87505, USA;Mars Center for Cocoa Science (MCCS), CP 55, Itajuipe, Bahia, 45630, Brazil;HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, AL, 35806, USA;Center for Genomics and Bioinformatics and School of Informatics and Computing, Indiana University, 919 E 10th St, Bloomington, IN, 47408, USA;Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA;Programa de Mejoramiento de Cacao, CATIE 7170, Turrialba, Costa Rica;United States Department of Agriculture-Agriculture Research Service, Genomics and Bioinformatics Research Unit, 141 Experiment Station Road, Stoneville, MS, 38776, USA;IBM T J Watson Research, Yorktown Heights, NY, 10598, USA;Estación Experimental Tropical Pichilingue, Instituto Nacional Autónomo de Investigaciones Agropecuarias (INIAP), Código Postal 24, Km 5 vía Quevedo - El Empalme, Quevedo, Ecuador;Clemson University Genomics Institute, 105 Collings Street, Clemson, SC, 29634, USA;Department of Biology, and Center for Genomics and Bioinformatics, Indiana University, 915 E. Third St, Bloomington, IN, 47405, USA;Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA;Department of Horticulture, Washington State University, Johnson Hall, Pullman, WA, 99164, USA;United States Department of Agriculture-Agriculture Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Rd, Miami, FL, 33158, USA

关键词: MYB113;    pod color;    genetic mapping;    haplotype phasing;    Matina 1-6;    genome;    Theobroma cacao L.;   

Others  :  1136512
DOI  :  10.1186/gb-2013-14-6-r53

 received in 2013-10-07, accepted in 2013-06-03,  发布年份 2013

【 摘 要 】

Background

Theobroma cacao L. cultivar Matina 1-6 belongs to the most cultivated cacao type. The availability of its genome sequence and methods for identifying genes responsible for important cacao traits will aid cacao researchers and breeders.

Results

We describe the sequencing and assembly of the genome of Theobroma cacao L. cultivar Matina

1-6. The genome of the Matina 1-6 cultivar is 445 Mbp, which is significantly larger than a sequenced Criollo cultivar, and more typical of other cultivars. The chromosome-scale assembly, version 1.1, contains 711 scaffolds covering 346.0 Mbp, with a contig N50 of 84.4 kbp, a scaffold N50 of 34.4 Mbp, and an evidence-based gene set of 29,408 loci. Version 1.1 has 10x the scaffold N50 and 4x the contig N50 as Criollo, and includes 111 Mb more anchored sequence. The version 1.1 assembly has 4.4% gap sequence, while Criollo has 10.9%. Through a combination of haplotype, association mapping and gene expression analyses, we leverage this robust reference genome to identify a promising candidate gene responsible for pod color variation. We demonstrate that green/red pod color in cacao is likely regulated by the R2R3 MYB transcription factor TcMYB113, homologs of which determine pigmentation in Rosaceae, Solanaceae, and Brassicaceae. One SNP within the target site for a highly conserved trans-acting siRNA in dicots, found within TcMYB113, seems to affect transcript levels of this gene and therefore pod color variation.

Conclusions

We report a high-quality sequence and annotation of Theobroma cacao L. and demonstrate its utility in identifying candidate genes regulating traits.

【 授权许可】

   
2013 Motamayor et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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