Identifying Candidate Genes for Cotton Fruit Branch Length Using BSA-Seq and RNA-Seq

Area of Science:

• Plant Genetics
• Molecular Biology
• Agricultural Science

Background:

• Fruit branch length in cotton is a critical trait affecting plant architecture and agricultural mechanization.
• Understanding the genetic basis of fruit branch length variation is essential for developing improved cotton varieties.

Purpose of the Study:

• To elucidate the molecular regulatory mechanisms underlying fruit branch length variation in upland cotton.
• To identify candidate genes controlling fruit branch length for future breeding applications.

Main Methods:

• An F2 segregating population was created from long- and short-fruit-branch cotton lines.
• Morphological, cytological, and omics approaches (BSA-Seq, RNA-Seq) were integrated for analysis.
• Bioinformatics and gene expression analyses were performed to identify candidate genes.

Main Results:

• Fruit branch length variation is primarily due to differences in cortical parenchyma cell elongation.
• BSA-Seq identified five QTL regions, and RNA-Seq revealed 3106 differentially expressed genes related to hormone signaling and cytoskeleton organization.
• GH_D02G0744 was identified as a highly probable candidate gene regulating cotton fruit branch length.

Conclusions:

• The study elucidates key genetic factors controlling cotton fruit branch length.
• Identified candidate genes provide a foundation for molecular breeding to optimize cotton plant architecture.