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Gene Study Aimed at Enhanced Cotton Fiber Breeding, Toolkits

08 November 2013

A new study by Texas A&M University cotton researchers and breeders will take advantage of new high-throughput sequencing technology to rapidly advance cotton genetics research and breeding.

Their goal: maintain U.S. cotton's competitiveness in the world cotton market, according to Dr. Hongbin Zhang, professor of plant genomics and systems biology and director of the Laboratory for Plant Genomics and Molecular Genetics in College Station.

The three-year, $500,000 National Institute for Food and Agriculture-funded study, will be conducted by Zhang, along with Dr. Meiping Zhang, Texas A&M AgriLife Research associate research scientist; Dr. C. Wayne Smith, Texas A&M professor of cotton breeding and soil and crop sciences associate department head, and Dr. Steve Hague, associate professor of cotton genetics and breeding in the Texas A&M AgriLife Research Cotton Improvement Lab.

"Cotton is the leading textile fiber and a major bioenergy oilseed crop in Texas and the U.S., with an annual economic impact of about $120 billion in the U.S.," Zhang said.

"In our previous studies, we have already constructed the first genome-wide physical map of Upland cotton, which accounts for more than 90 percent of the cotton in Texas and the U.S." he said. "We are also using the physical map as a platform to sequence the cotton genome."

Also, they previously developed a population of 1,172 recombinant inbred lines that are essential to fine map the cotton genome and genes of economic importance for fiber and oilseed production, Zhang said.

They phenotyped seven of the traits important for fiber quality and yield in 200 of those lines and their parents using three replicated field trials for three years at College Station. The researchers then sequenced and profiled the gene expressions in the developing fibers of those lines, Zhang said.

"Now we want to develop a new and advanced breeding system in cotton, such as gene-based breeding, where we are selecting the target traits based on the genes controlling the traits, gene activities and gene interaction networks."

The long-term goals are to clone the genes that control all major traits of cotton fiber quality and fiber yield, determine their molecular basis and regulation mechanisms, and develop fiber gene-based toolkits, enabling enhanced cotton fiber breeding, he said.

The breeding toolkits to be developed will enhance breeding for all major cotton fiber traits, including fiber yield, lint percent, fiber length, strength, micronaire, uniformity and elongation across the U.S. cotton breeding programs, Zhang said.

This study, he said, will be used to advance research efforts toward cloning and molecular characterization of the genes and trait locations important for fiber quality and yield. Also, the study will develop a "golden" standard genome sequence for Upland cotton from the sequences previously generated by this and other cotton research programs.

Zhang said if they can decipher the molecular basis of cotton fiber quality and yield, a gene-based advanced and efficient cotton breeding program could be developed.

In this new study, the team will further phenotype the 200 lines and parents for the seven major fiber quality and yield component traits in replicated field trials for two years at two additional locations in the U.S. Cotton Belt - Lubbock and Saint Joseph, La. - using the high volume instrument.

This will allow the genetic variation of the traits to be measured accurately and the genes controlling the traits to be mapped reliably, he said.

Zhang said more than 800 fiber samples will be collected from the field trials of the 200 lines. The samples can be phenotyped in five major fiber quality component traits within an eight-hour day using the high volume machine.

Using the Restriction site-Associated DNA sequencing technology that they established in their lab, they will genotype the 200 lines and parents and a panel of 50-100 cotton breeding or germplasm lines widely used in the U.S. cotton breeding programs.

The sequencing and fiber quality and yield data will be analyzed to identify single nucleotide polymorphism, or SNP, markers across the cotton genome, construct a high-density SNP marker map for cotton, map the genes controlling the fiber traits and develop DNA toolkits for enhanced cotton breeding.

Furthermore, since a panel of 50-100 cotton breeding or germplasm lines widely used in the U.S. cotton breeding programs will be sequenced using the same technology, the toolkits developed in the project can be quickly transferred to and used by their and other cotton breeding programs.

When the study is complete, Zhang and his team expect to have a high-density genetic map for cotton that consists of more than 10,000 genomic SNPs and more than 2,000 "10-days past anthesis" fiber expressed gene SNPs, yielding a marker density map four-fold higher than those of existing cotton genetic maps.

The resultant genetic map of this project will be combined with the physical map and genome sequence of cotton previously developed, he said. Together, these are expected to provide comprehensive and integrated platforms and tools for advanced cotton genetics research and enhanced cotton breeding.

November 2013

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