Research Genome Research

Contact Dr. Qingyi Yu at QYu@ag.TAMU.edu for information about The Dallas Center's genome research program.

About

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The Dallas Center genomics research team

The Genomics team of the Texas A&M AgriLife Research and Extension Center at Dallas focuses on applying genomics and molecular genetics to crop improvement, with an emphasis on tropical and subtropical crops. The team is comprised of researchers with expertise in bioinformatics, evolutionary genomics, genetics, and molecular biology. Current researchtopics include genomic dissection of the polyploidy sugarcane genome for energy cane improvement, flower development and sex chromosome evolution in Caricaceae, genomics of abiotic stress tolerance in warm-season turfgrass, and gene regulatory networks underlying CAM photosynthesis in pineapple.

Genomics Resources

TAIR - The Arabidopsis Information Resource maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Click to visit TAIR

CoGe - a platform for performing comparative genomics research, providing an open-ended network of interconnected tools to manage, analyze, and visualize next-gen data. Click to visit CoGe

JGI Phytozome - the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, and selected genomes and datasets sequenced elsewhere. Click to visit JGI Phytozome

PlantGDB - A collection of tools and resources for plant genomics. Click to visit PlantGDB

NCBI - National Center for Biotechnology Information provides access to biomedical and genomic information.Click to visit NCBI

Plant TFDB - Plant Transcription Factor Database. Click to visit Plant TFDB

Research Areas

Genomic dissection of complex traits in polyploid sugarcane to improve sugar and bioenergy production

bamboo in a row bug's eye view

As a C4 plant, sugarcane (Saccharum spp. Poaceae) has been recognized as one of the world’s most efficient crops in converting solar energy into chemical energy. Sugarcane is also among the crops having the most favorable input/output ratios. However, the large genome size, high ploidy level, interspecific hybridization and aneuploidy make sugarcane one of the most complex genomes and have long hampered genome research in sugarcane. Modern sugarcane cultivars are derived from interspecific hybridization between S. officinarum and S. spontaneum with 80-90% of the genome from S. officinarum and 10-20% of the genome from S. spontaneum. We are using genomics tools to dissect the complex polyploidy sugarcane genome and study allelic variations of major genes affecting biomass yield in sugar cane aiming to understand the complex mechanisms leading to the superior productivity of sugarcane.

Flower development and sex chromosome evolution in caricaceae

papaya flower macro close up

Unlike most animal species that produce unisexual individuals, the majority of flowering plants produce flowers that are ‘perfect’ and contain both ‘male’ and ‘female’ organs. Less than 10% of plant species produce flowers, which are unisexual. Papaya is a polygamous plant species producing both dioecious and perfect flowers and provides an opportunity for comparative analysis of flower development in dioecious and hermaphrodite plant species.

The sex determination system in papaya is particularly intriguing, not only because it has three sex types within the species, also because it shows frequent sex reversal caused by environmental factors. Recent studies showed that sex determination in papaya is controlled by a pair of primitive sex chromosomes. We are cloning the sex determination genes in papaya and performing comparative genomics analysis to understand the origin and evolution of sex chromosomes in Caricaceae.

Genomics of abiotic stress tolerance in warm-season turfgrasses

turfgrass germplasm on black background

Turfgrass is the largest irrigated crop and the 2nd largest seed crop in the United States with about $57.9 billion annual production value. It was estimated that the total acreage of turfgrass in the United States was approximately 50 million acres, an area larger than the total acreage for cotton, sorghum, barley, and oats. As drinking water becomes more and more scarce, developing turfgrass cultivars with reduced water demands and/or cultivars that can tolerate effluent or brackish water leaving fresh water for municipal needs becomes a high priority.

The long-term scientific goal of the project is to determine the gene regulatory network that regulates salt tolerance in Zoysia matrella. Results of this research will significantly advance our understanding of the genetic and molecular basis of salt tolerance in zoysiagrass, and will be critical for designing strategies to develop turfgrass for the future.

Dallas Genomics Team

Dr. Qingyi Yu

Dr. Qingyi Yu portrait

Principal Investigator, Associate Professor, Plant Pathology
Dallas Genome Studies
Texas A&M AgriLife Research
qyu@ag.tamu.edu
972.952.9225

Dr. Ratnesh Singh

Dr. Ratnesh Singh portrait

Assistant Research Scientist
Dallas Genome Studies
Texas A&M AgriLife Research
ratnesh.singh@ag.tamu.edu
972.952.9234

Dr. Anupma Sharma

Dr. Anupma Sharma portrait

Postdoctoral Research Associate
Dallas Genome Studies
Texas A&M AgriLife Research
anupma.sharma@ag.tamu.edu
972.952.9234

Dr. Fangfang Wang

Dr. Fang Fang Wang portrait

Postdoctoral Research Associate
Dallas Genome Studies
Texas A&M AgriLife Research
fangfang.wang@ag.tamu.edu
972.952.9234

Haritha Dhanikonda

Haritha Dhanikonda portrait

Technician I
Dallas Genome Studies
Texas A&M AgriLife Research
Haritha.Dhanikonda@ag.tamu.edu
972.952.9234

Juan Liu

Juan Li portrait

Visiting Research Scholar
Dallas Genome Studies
Texas A&M AgriLife Research
Juan.Liu@ag.tamu.edu
972.952.9234

Select Publications

Find a comprehensive list of Dr. Qingyi Yu's publications at Google Scholar

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