Utilization of the Cotton and Genome Sequence of Gossypium Barbadense for Discovery of Rare Alleles in Upland Cotton Derived From G. Barbadense

Project Director
SCHEFFLER B E

Recipient Organization
AGRICULTURAL RESEARCH SERVICE
(N/A)
STONEVILLE,MS 38776

Performing Department
(N/A)

Non Technical Summary
(N/A)

Animal Health Component

(N/A)

Research Effort Categories

Basic

50%

Applied

50%

Developmental

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
201	1710	1040	100%

Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1710 - Upland cotton;

Field Of Science
1040 - Molecular biology;

Keywords

Goals / Objectives
The diploid reference sequence has fundamentally changed cotton research. Application of this reference sequence to improve our understanding of the polyploid, cotton genome has been rapid. These basic advances will further our progress of improving the production of U.S. domestic cotton by 1) allowing us to associate traits to one of two duplicated genomes and enabling their selection during breeding and 2) understand the origin of and frequency of introgressed alleles within the Gossypium (G.) hirsutum genome.

Project Methods
Proposed is a significant re-sequencing project by sequencing many accessions of Gossypium (G.) barbadense at relatively low coverage (5x). The justification of re-sequencing G. barbadense instead of G. hirsutum is found in sequence capture data. When examining a hirsutum diversity panel, occasionally rare alleles are found - even in accessions that should not be that diverse. These 'rare' alleles could be introgressions from G. barbadense and while rare in the hirsutum germplasm, they really are not rare alleles within cotton germplasm as a whole. Thus, a solid database of G. barbadense sequence will allow hirsutum to researchers make a value judgment regarding the 'rare' alleles introgressed from G. barbadense. Such a judgment cannot happen without some G. barbadense sequence. There is ample evidence and a history of introgression from G. barbadense in SeaLand cottons and the PeeDee germplasm collections to justify this approach.

Progress 10/01/12 to 09/30/13

Outputs
Progress Report Objectives (from AD-416): The diploid reference sequence has fundamentally changed cotton research. Application of this reference sequence to improve our understanding of the polyploid, cotton genome has been rapid. These basic advances will further our progress of improving the production of U.S. domestic cotton by 1) allowing us to associate traits to one of two duplicated genomes and enabling their selection during breeding and 2) understand the origin of and frequency of introgressed alleles within the Gossypium (G.) hirsutum genome. Approach (from AD-416): Proposed is a significant re-sequencing project by sequencing many accessions of Gossypium (G.) barbadense at relatively low coverage (5x). The justification of re-sequencing G. barbadense instead of G. hirsutum is found in sequence capture data. When examining a hirsutum diversity panel, occasionally rare alleles are found - even in accessions that should not be that diverse. These 'rare' alleles could be introgressions from G. barbadense and while rare in the hirsutum germplasm, they really are not rare alleles within cotton germplasm as a whole. Thus, a solid database of G. barbadense sequence will allow hirsutum to researchers make a value judgment regarding the 'rare' alleles introgressed from G. barbadense. Such a judgment cannot happen without some G. barbadense sequence. There is ample evidence and a history of introgression from G. barbadense in SeaLand cottons and the PeeDee germplasm collections to justify this approach. The goal of this project is to develop genomics resources specifically in relation to understanding the genome of long-staple cottons from the species Gossypium barbadense by looking for rare and important alleles. Seven Gossypium barbadense accessions were selected for a technique called resequencing, which basically generates most of the DNA sequence of an individual but in an unorganized way. Organization and comparison then takes place by comparing the sequence data of Gossypium barbadense to the reference genome Gossypium ramodii. DNA sequencing libraries of the seven accessions has taken place and are now in the high-throughput DNA sequencing queue. This work is being done in conjunction with Brigham Young University. Participants converse through mainly emails, quarterly reports, face to face meetings or phone conversations.

Impacts
(N/A)

Publications