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ARS Home » Southeast Area » New Orleans, Louisiana » Southern Regional Research Center » Cotton Fiber Bioscience Research » Research » Publications at this Location » Publication #400571
Research Project: Molecular Characterization and Phenotypic Assessments of Cotton Fiber Quality Traits

Location: Cotton Fiber Bioscience Research

Title: Genomics-based breeding

Author
item Fang, David

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 7/10/2025
Publication Date: 10/4/2025
Citation: Fang, D.D. 2025. Genomics-based breeding. Book Chapter. The Cotton Genome P.109-127. https://doi.org/10.1007/978-3-031-84605-2_7.
DOI: https://doi.org/10.1007/978-3-031-84605-2_7

Interpretive Summary: Rapid advancement in DNA and genomic technologies in the last decade has greatly facilitated application of marker assisted selection (MAS) and exploitation of genomic selection (GS) in cotton breeding. In this chapter, I first discussed the technological foundations for successful MAS and GS discoveries. These include high quality genome assemblies of diploid and tetraploid cotton species, SNP arrays with variable number of markers, novel populations for trait analysis and new methods to analyze gene functions. Then I reviewed recent studies in trait QTL analysis and gene identification using genome wide association study (GWAS) and transcriptome wide association study (TWAS) with focus on my own research of analyzing MAGIC population. I suggest that epistasis is a major contributor to the fiber phenotypic variance. Next, I provided brief summary on MAS application in cotton breeding, and GS research in cotton. MAS has been widely used to assist selection of traits controlled by major genes such as disease resistance and fiber strength and length. Although GS research is still at the early stage in cotton, it holds great potential for quantitative trait improvement. Genomics-based breeding techniques will not only advance our knowledge in basic science but also speed up breeding process with reduced cost.

Technical Abstract: Rapid advancement in DNA and genomic technologies in the last decade has greatly facilitated application of marker assisted selection (MAS) and exploitation of genomic selection (GS) in cotton breeding. In this chapter, I first discussed the technological foundations for successful MAS and GS discoveries. These include high quality genome assemblies of diploid and tetraploid cotton species, SNP arrays with variable number of markers, novel populations for trait analysis and new methods to analyze gene functions. Then I reviewed recent studies in trait QTL analysis and gene identification using genome wide association study (GWAS) and transcriptome wide association study (TWAS) with focus on my own research of analyzing MAGIC population. I suggest that epistasis is a major contributor to the fiber phenotypic variance. Next, I provided brief summary on MAS application in cotton breeding, and GS research in cotton. MAS has been widely used to assist selection of traits controlled by major genes such as disease resistance and fiber strength and length. Although GS research is still at the early stage in cotton, it holds great potential for quantitative trait improvement. Genomics-based breeding techniques will not only advance our knowledge in basic science but also speed up breeding process with reduced cost.