# Construction of BAC contig maps of homoeologous chromosomes A12 and D12 of Gossypium hirsutum L. acc. TM-1

## TL;DR

This paper constructs a detailed map of cotton chromosomes A12 and D12 using BAC clones and optimized software parameters.

## Contribution

A new method for optimizing FPC software parameters is introduced to distinguish homoeologous chromosome segments in cotton.

## Key findings

- A BAC contig map of cotton chromosomes A12 and D12 was successfully constructed.
- Optimized FPC parameters enabled separation of homoeologous chromosome segments.
- The approach provides a platform for genome-wide and evolutionary studies in cotton.

## Abstract

The Gossypium hirsutum homoeologous chromosome 12 encodes important genes that contribute to fiber fuzz, lethality, gland development and male sterility. In this study a physical map of the cotton TM-1 chromosome 12 was constructed. A number of large-insert cotton genome libraries are available, and genome-wide physical mapping using large insert segments combined with bacterial cloning is a thriving area of genome research. However, sequencing of the cotton genome is difficult due to sequence repeats and homoeologous regions. In order to effectively distinguish the homologous segments, a new method for adjusting the parameters of the FPC software was applied for contig map construction.

All available markers on chromosomes A12 and D12 were used to screen the TM-1 BAC library by PCR. A total of 775 clones (387 for A12, 388 for D12) were obtained using Hind III fingerprinting and used for construction of the contig map. Seven pairs of SSR markers located on A12 and D12 were chosen for contig analysis. Following optimization of the tolerance (10) and cutoff (1e-12) parameters, combining all clones from A12 and D12 produced two separate contigs.

The BAC contig map of chromosomes A12 and D12 was constructed and FPC software parameters were optimized for analysis. The resulting approach is a powerful platform for genome-wide and evolutionary research on cotton.