Juan Carlos Motamayor Arias
,
MARS Inc., Miami, FL
Keithanne Mockaitis
,
Indiana University, Bloomington, IN
Jeremy Schmutz
,
HudsonAlpha Institute for Biotechnology, Huntsville, AL
Niina Haiminen
,
IBM T J Watson Research - Computational Biology Center, Yorktown Heights, NY
Donald Livingstone III
,
MARS Inc., Miami, FL
Omar Cornejo
,
Stanford University, Stanford, CA
Seth David Findley
,
Mars, Inc., Miami, FL
Ping Zheng
,
Washington State University, Pullman, WA
Filippo Utro
,
IBM Research, Yorktown Heights, NY
Stefan Royaert
,
USDA ARS SHRS, Miami, FL
Christopher Saski
,
Clemson University Genomics Institute, Clemson, SC
Jerry Jenkins
,
DOE Joint Genome Institute, Huntsville, AL
Ram Podicheti
,
School of Informatics and Computing, Indiana University, Bloomington, IN
Meixia Zhao
,
Purdue University, West Lafayette, IN
Brian Scheffler
,
USDA-ARS-MSA, Stoneville, MS
Alex Feltus
,
Genetics & Biochemistry, Clemson University, Clemson, SC
Fredy M. Amores
,
INIAP, Ecuador, Guayaquil, Ecuador
Wilbert Phillips
,
Centro Agronomico Tropical de Investigacion, Cartago, Costa Rica
Jean-Philippe Marelli
,
Mars Center for Cocoa Science (MCCS), Barro Preto, BA, Brazil
Gregory D. May
,
National Center for Genome Resources, Santa Fe, NM
Howard-Yana Shapiro
,
University of California, Davis, Davis, CA
Jianxin Ma
,
Purdue University, West Lafayette, IN
Carlos Bustamante
,
Stanford University, stanford, CA
Raymond J. Schnell
,
MARS Inc., Miami, FL
Dorrie Main
,
Washington State University, Pullman, WA
Don Gilbert
,
Department of Biology, Indiana University, Bloomington, IN
Laxmi Parida
,
IBM T J Watson Research - Computational Biology Center, Yorktown Heights, NY
David N. Kuhn
,
USDA ARS SHRS, Miami, FL
Background: Matina 1-6 belongs to the most cultivated cacao type worldwide. Availability of its genome sequence and methods for identifying genes responsible for important cacao traits promise to greatly aid cacao researchers and breeders. A preliminary version of the
Theobroma cacao L. Matina 1-6 genome (V0.9) was released to the public in 2010.
Results: The Matina 1-6 genome is 445 Mbp, significantly larger than a recently sequenced Criollo cultivar, and similar in size to other cacao cultivars. Here, we describe the sequencing and assembly of the nucleotide sequence of the Matina 1-6 genome (V1.1), which contains 711 scaffolds that cover 346.0 Mbp of the genome, 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. Together with a novel phasing method used to reliably derive parental haplotypes, association mapping and gene expression analyses, we leverage this robust reference genome to identify a candidate gene responsible for pod color variation. We demonstrate that green/red pod color in cacao, is likely regulated by a gene encoding an R2R3 MYB transcription factor (TcMYB113), homologs of which determine organ pigmentation in Rosaceae, Solanaceae, and Brassicaceae. One SNP within the target site for a highly conserved transacting siRNA in dicots found within TcMYB113 seems to affect transcript levels and therefore pod color variation.
Conclusions: This report documents our high-quality sequence and annotation of the Matina 1-6 genome and demonstrates its utility to identify candidate genes regulating traits when combined with our comprehensive haplotype mapping approach.
