A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

Title: Quantile-quantile (Q-Q) Plot of six fiber traits generated from GWAS analysis following mixed linear model (MLM) using GAPIT software. A) Fiber elongation (ELO), B) Micronaire (MIC), C) Short fiber content (SFC), D) Fiber strength (STR), E) Upper half mean fiber length (UHM), and F) Uniformity index (UI). Description of data: Q-Q plots of six fiber traits generated from GWAS analysis following MLM are included in this figure. The X and Y axis have the expected and observed negative logarithm 10 of p value, respectively generated during GWAS analysis. (DOCX 207 kb

Recent Developments in Fiber Genomics of Tetraploid Cotton Species

Cotton (Gossypium spp.) produces naturally soft, single-celled trichomes as fiber on the seed coat supplying the main source of natural raw material for the textile industry. It is economically considered as one of the most leading cash crops in the world and evolutionarily very important as a model system for detailed scientific investigations. Cotton production is going through a big transition stage such as losing the market share in competition with the synthetic fibers, high popularity of Bt and herbicide resistance genes in cotton cultivars, and the recent shift of fiber demands to meet the standard fiber quality due to change of textile technologies to produce high superior quality of fibers in the global market. Recently, next-generation sequencing technologies through high-throughput sequencing at greatly reduced costs provided opportunities to sequence the diploid and tetraploid cotton genomes. With the availability of large volume of literatures on molecular mapping, new genomic resources, characterization of cotton genomes, discoveries of many novel genes, regulatory elements including small and microRNAs and new genetic tools such as gene silencing or gene editing technique for genome manipulation, this report attempted to provide the readers a comprehensive review on the recent advances of cotton fiber genomics research

A High-Throughput Standard PCR-Based Genotyping Method for Determining Transgene Zygosity in Segregating Plant Populations

In crop research programs that implement transgene-based strategies for trait improvement it is necessary to distinguish between transgene homozygous and hemizygous individuals in segregating populations. Direct methods for determining transgene zygosity are technically challenging, expensive, and require specialized equipment. In this report, we describe a standard PCR-based protocol coupled with capillary electrophoresis that can identify transgene homozygous and hemizygous individuals in a segregating population without knowledge of transgene insertion site. PCR primers were designed to amplify conserved T-DNA segments of the 35S promoter, OCS terminator, and NPTII kanamycin resistance gene in the pHellsgate-8 RNAi construct for the Gossypium hirsutum phytochrome A1 gene. Using an optimized multiplexed reaction mixture and an amplification program of only 10 cycles we could discriminate between transgene homozygous and hemizygous cotton control DNA samples based on PCR product peak characteristics gathered by capillary electrophoresis. The protocol was refined by evaluating segregating transgenic progeny from nine BC1S1 populations derived from crosses between the transgenic cotton parent ‘E-1-7-6’ and other cotton cultivars. OCS PCR product peak height and peak area, normalized by amplification of the native cotton gene GhUBC1, revealed clear bimodal distributions of OCS product characteristics for each BC1S1 population indicating the presence of homozygous and hemizygous clusters which was further confirmed via K-means clustering. BC1S1 plants identified as homozygous or hemizygous were self-fertilized to produce BC1S2 progeny. For the homozygous class, 19/20 BC1S2 families confirmed the homozygous BC1S1 prediction while 21/21 BC1S2 families confirmed the hemizygous prediction of the original parent. This relatively simple protocol provides a reliable, rapid, and high-throughput way of evaluating segregating transgenic populations using methods and equipment common to crop molecular breeding labs