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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT OF AN INTERNATIONAL MARKER ASSISTED SELECTION PROGRAM FOR CACAO

Location: Subtropical Horticulture Research

Title: Increasing the efficiency of traditional cacao breeding using whole genome sequencing information.

Authors
item Schnell Ii, Raymond
item Brown, James
item KUHN, DAVID
item TONDO, CECILE
item Motamayor, H. - MARS, INC.
item Shapiro, Howard-Yana - MARS, INC.
item Scheffler, Brian - USDA-ARS MSA GENOMICS LAB
item Main, Dorrie - WSU, DEP OF HORT&LNDSC AR
item Isidore, Rigoutsos - IBM, WATSON RES CENTER

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: January 12, 2009
Publication Date: January 12, 2009
Citation: Schnell Ii, R.J., Brown, J.S., Kuhn, D.N., Tondo, C.L., Motamayor, H.Y., Shapiro, H., Scheffler, B., Main, D., Isidore, R. 2009. Increasing the efficiency of traditional cacao breeding using whole genome sequencing information.. Plant and Animal Genome Conference.

Technical Abstract: Unfortunately, 80% of the genotypes from the "hybrid seeds" are unproductive in farmers' fields. In 1999 the USDA and Mars Inc. initiated a Marker Assisted Selection (MAS) program for cacao that has reduces many of the problems in traditional breeding. One limitation of the MAS program is the distance, between flanking markers that identify Quantitive Trait Loci (QTLs) for disease resistance, quality, and productivity traits. Developing markers more tightly linked to QTL or in the genes themselves would enhance MAS. Whole genome sequencing is economical for high value crops and having the complete genome sequence of cacao will greatly enhance the MAS effort. A combination of Sanger, 454 and Illumina sequencing methodologies are being used. A highly homozygous cultivar, 'Matina 1-6, was chosen for whole genome sequencing. Another 20 clones from diverse genetic groups will be partially sequenced using 454 technology to identify Single Nucleotide Polymorphisms (SNP). The development of thousands of SNP markers will allow complete saturation of the genetic linkage map and much closer associations of specific alleles with (QTL) for disease resistance, productivity, plant architecture and quality characteristics. These markers will greatly enhance the current (MAS) program allowing increased efficiency in field selection of new cultivars.

Last Modified: 9/10/2014