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United States Department of Agriculture

Agricultural Research Service

Research Project: Identification of Est-Ssr and Snp Markers for Linkage Mapping in Dioscorea Alata L.(YAM)

Location: Genomics and Bioinformatics Research Unit

2013 Annual Report


1a.Objectives (from AD-416):
Preliminary Quantitative Trait Loci (QTL) mapping studies associated with anthracnose resistance and tuber quality in yam while generating SNPs for yam.


1b.Approach (from AD-416):
RNA - seq analysis of complementary Deoxyribonucleic Acid (cDNA) from resistant, susceptible genotypes and First filial generations (F1) using Illumina technology, genotyping and validation.


3.Progress Report:

The goal of this project is to develop genomics resources for improving yam breeding.

Exploratory research is being conducted with the International Institute of Tropical Agriculture (IITA) as part of an agreement. Yam is an important crop in Africa but has limited genomic resources. Bioinformatic analysis was conducted on yam for Simple Sequence Repeats (SSRs) with the goal to identify those in the non-coding region in the hope they will be more variable than those in coding regions. A sub-set was tested on mapping parents provided by IITA. Validated DNA markers were processed on a yam mapping population related to anthracnose resistance and in FY 2012 140 SSRs were processed and in FY 2013 325 SSRS were run and are presently being analyzed.

To date, it has not been possible to ship messenger Ribonucleic acid (mRNA) that has remained stable through the shipping process for RNASeq (gene expression technique) analysis. Leaf samples sent from IITA to Stoneville, MS, have also not survived the shipping process for good mRNA extraction. The preparation of Illumina RNASeq libraries is beyond the present capabilities of IITA due the lack of specialized equipment or the kits. Efforts are presently under way to try new mRNA extractions with new leaf material.

DNA of the two mapping parents of the IITA genetic population were subject to whole genome sequencing using sheared DNA and subject to two lanes of 2 X 100 bp reads Illumina sequencing on a HiSeq 2000. The number of reads for parent one were 849,524,270 and parent two 530,269,368. Genomic DNA sequences of yam parents were put into the DNA assembler program CLC Bio using default parameters. The assembled data should be of sufficient quality to be used to gain insight into gene spacing, and can be uses as a sequence database for BLAST searches to find genes of interest. The data can also be used for identification of Single Nucleotide Polymorphisms (SNPs) between the two parents or other yam lines. The ratio of nucleotides from both agencies show an extreme bias for the genome of Dioscorea alata L. to be AT rich (~64%). This will impact the strategy of any genome project on yams.

Work exchange takes place by email and phone conversations.


Last Modified: 11/28/2014
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