Roy G. Cantrell

Toward Sequencing Cotton (Gossypium) Genomes

Despite rapidly decreasing costs and innovative technologies, sequencing of angiosperm genomes is not yet undertaken lightly. Generating larger amounts of sequence data more quickly does not address the difficulties of sequencing and assembling complex genomes de novo. The cotton ( Gossypium spp.)

CMD: a Cotton Microsatellite Database resource for Gossypium genomics

BackgroundThe Cotton Microsatellite Database (CMD) http://www.cottonssr.org is a curated and integrated web-based relational database providing centralized access to publicly available cotton microsatellites, an invaluable resource for basic and applied research in cotton breeding.DescriptionAt present CMD contains publication, sequence, primer, mapping and homology data for nine major cotton microsatellite projects, collectively representing 5,484 microsatellites. In addition, CMD displays data for three of the microsatellite projects that have been screened against a panel of core germplasm. The standardized panel consists of 12 diverse genotypes including genetic standards, mapping parents, BAC donors, subgenome representatives, unique breeding lines, exotic introgression sources, and contemporary Upland cottons with significant acreage. A suite of online microsatellite data mining tools are accessible at CMD. These include an SSR server which identifies microsatellites, primers, open reading frames, and GC-content of uploaded sequences; BLAST and FASTA servers providing sequence similarity searches against the existing cotton SSR sequences and primers, a CAP3 server to assemble EST sequences into longer transcripts prior to mining for SSRs, and CMap, a viewer for comparing cotton SSR maps.ConclusionThe collection of publicly available cotton SSR markers in a centralized, readily accessible and curated web-enabled database provides a more efficient utilization of microsatellite resources and will help accelerate basic and applied research in molecular breeding and genetic mapping in Gossypium spp.

Effects of Chromosome-Specific Introgression in Upland Cotton on Fiber and Agronomic Traits

Interspecific chromosome substitution is among the most powerful means of introgression and steps toward quantitative trait locus (QTL) identification. By reducing the genetic “noise” from other chromosomes, it greatly empowers the detection of genetic effects by specific chromosomes on quantitative traits. Here, we report on such results for 14 cotton lines (CS-B) with specific chromosomes or chromosome arms from G. barbadense L. substituted into G. hirsutum and chromosome-specific F2 families. Boll size, lint percentage, micronaire, 2.5% span length, elongation, strength, and yield were measured by replicated field experiments in five diverse environments and analyzed under an additive–dominance (AD) genetic model with genotype and environment interaction. Additive effects were significant for all traits and dominance effects were significant for all traits except 2.5% span length. CS-B25 had additive effects increasing fiber strength and fiber length and decreasing micronaire. CS-B16 and CS-B18 had additive effects related to reduced yields. The results point toward specific chromosomes of G. barbadense 3-79 as the probable locations of the genes that significantly affect quantitative traits of importance. Our results provided a scope to analyze individual chromosomes of the genome in homozygous and heterozygous conditions and thus detected novel effects of alleles controlling important QTL.

Sampling nucleotide diversity in cotton

BackgroundCultivated cotton is an annual fiber crop derived mainly from two perennial species, Gossypium hirsutum L. or upland cotton, and G. barbadense L., extra long-staple fiber Pima or Egyptian cotton. These two cultivated species are among five allotetraploid species presumably derived monophyletically between G. arboreum and G. raimondii. Genomic-based approaches have been hindered by the limited variation within species. Yet, population-based methods are being used for genome-wide introgression of novel alleles from G. mustelinum and G. tomentosum into G. hirsutum using combinations of backcrossing, selfing, and inter-mating. Recombinant inbred line populations between genetics standards TM-1, (G. hirsutum) × 3-79 (G. barbadense) have been developed to allow high-density genetic mapping of traits.ResultsThis paper describes a strategy to efficiently characterize genomic variation (SNPs and indels) within and among cotton species. Over 1000 SNPs from 270 loci and 279 indels from 92 loci segregating in G. hirsutum and G. barbadense were genotyped across a standard panel of 24 lines, 16 of which are elite cotton breeding lines and 8 mapping parents of populations from six cotton species. Over 200 loci were genetically mapped in a core mapping population derived from TM-1 and 3-79 and in G. hirsutum breeding germplasm.ConclusionIn this research, SNP and indel diversity is characterized for 270 single-copy polymorphic loci in cotton. A strategy for SNP discovery is defined to pre-screen loci for copy number and polymorphism. Our data indicate that the A and D genomes in both diploid and tetraploid cotton remain distinct from each such that paralogs can be distinguished. This research provides mapped DNA markers for intra-specific crosses and introgression of exotic germplasm in cotton.

Linkage Map Construction and Quantitative Trait Locus Analysis of Agronomic and Fiber Quality Traits in Cotton

The superior fiber properties of Gossypium barbadense L. serve as a source of novel variation for improving fiber quality in Upland cotton (G. hirsutum L.), but introgression from G. barbadense has been largely unsuccessful due to hybrid breakdown and a lack of genetic and genomic resources. In an effort to overcome these limitations, we constructed a linkage map and conducted a quantitative trait locus (QTL) analysis of 10 agronomic and fiber quality traits in a recombinant inbred mapping population derived from a cross between TM‐1, an Upland cotton line, and NM24016, an elite G. hirsutum line with stabilized introgression from G. barbadense. The linkage map consisted of 429 simple‐sequence repeat (SSR) and 412 genotyping‐by‐sequencing (GBS)‐based single‐nucleotide polymorphism (SNP) marker loci that covered half of the tetraploid cotton genome. Notably, the 841 marker loci were unevenly distributed among the 26 chromosomes of tetraploid cotton. The 10 traits evaluated on the TM‐1 × NM24016 population in a multienvironment trial were highly heritable, and most of the fiber traits showed considerable transgressive variation. Through the QTL analysis, we identified a total of 28 QTLs associated with the 10 traits. Our study provides a novel resource that can be used by breeders and geneticists for the genetic improvement of agronomic and fiber quality traits in Upland cotton.

Resistance gene analogue markers are mapped to homeologous chromosomes in cultivated tetraploid cotton

Degenerate primers designed from conserved motifs of known plant resistance gene products were used to amplify genomic DNA sequences from the root-knot nematode (Meloidogyne incognita) resistance genetic source, Upland cotton (Gossypium hirsutum) cultivar Auburn 634 RNR. A total of 165 clones were isolated, and sequence analysis revealed 57 of the clones to be novel nucleotide sequences, many containing the resistance (R)-protein nucleotide-binding site motif. A cluster analysis was performed with resistance gene analogue (RGA) nucleotide sequences isolated in this study, in addition to 99 cotton RGA nucleotide sequences already deposited in GenBank, to generate a phylogenetic tree of cotton R genes. The cotton RGA nucleotide sequences were arranged into 11 groups and 56 sub-groups, based on genetic distances. Multiple sequence alignments were performed on the RGA sequences of each sub-group, and either the consensus sequences or individual RGA sequences were used to design 61 RGA-sequence-tagged site primers. A recombinant inbred line (RIL) population of cultivated tetraploid cotton was genotyped using RGA-specific primers that amplified polymorphic fragments between the two RIL parents. Nine RGA markers were mapped to homeologous chromosomes 12 and 26, based on linkage to existing markers that are located on these chromosomes.

Inheritance of fiber quality and lint yield in a chemically mutated population of cotton

The narrow germplasm base of the upland cotton (Gossypium hirsutum L.), grown on the Texas high plains historically, has limited improvement of fiber quality. Chemical mutagenesis and subsequent selection have helped the development of lines with improved fiber quality in cultivars adapted to this region. This study was conducted to determine the inheritance of improvements in fiber quality. M3 lines with divergent fiber properties of micronaire, length, and strength were selected from a population of Paymaster HS 200 treated with 3% v/v ethyl methanesulfonate (EMS) for two hours. The 115 selected lines of M4 and M5 generation were evaluated for fiber quality and lint yield. Regression of the M4 and M5 on the M3 generation, as well as the M5 on the M4 was used to generate narrow sense heritability coefficients. Significant variations were observed between the mutant lines in all generations except for lint yield in the M5 (1997). The highest heritability estimates were found in fiber length (h2= 0.29** to 0.46**). Micronaire and strength showed intermediate heritability estimates of h2= 0.14 to 0.19, while lint yield had a very low heritability estimate of h2= 0.03. Fiber length and strength were correlated (r= 0.58** to 0.46**) in all the three generations. The mutants identified in these studies have the potential to improve fiber quality of upland cotton without introducing alien genes that may reduce adaptation to short growing season production regions.