High-Density SNP Genotyping Applied to Interspecific Germplasm in Upland Cotton (Gossypium Hirsutum L.): (I.) CSB17 Chromosome-Specific RIL Analysis and (II.) G. Mustelinum (Miers Ex Watt) Linkage Mapping
Abstract
The narrow genetic base of Upland cotton has slowed growth of its productivity as
a crop and perhaps also its use in the world. The need to broaden genetic diversity of
Upland cotton is urgent, especially given the contemporary need to improve
competitiveness of the fiber attributes, productivity and sustainability. The advent of
high-density high-throughput molecular marker genotyping in cotton using the
CottonSNP63K array has revolutionized the resolution and accuracy of genetic analysis
in cotton. In this study, the CottonSNP63K array is used to analyze two populations,
one a set of interspecific chromosome-specific RILs and the other an early-generations
interspecific mapping population, both at the 52-chromosome level.
A chromosome linkage map was derived from 50 isogenic chromosome-specific
recombinant inbred lines, which were derived from a cross between a disomic
substitution line CS-B17 homozygous for G. barbadense ‘3-79’ chromosome 17 and its
recurrent parent TM-1. Fiber quality and Fusarium wilt race 4 resistance data on the
lines were subjected to quantitative trait locus (QTL) analysis. Results indicated that
the CS-RIL approach affords high sensitivity, in that it detected seven fiber quality
QTLs in chromosome 17, whereas none had been found previously by analysis of
conventional TM-1/3-79 populations. However, one lint% QTL was detected previously
using a similarly interspecific population. A single locus accounted for multiple FOV4
resistance trait QTLs and corresponded to previous research. In this CS-RIL study, QTLs exhibited exceptionally high R^2 values and consistency across experiments,
reflecting avoidance of genetic background noise and GxE interactions.
The first high-resolution SNP-based genetic map between G. hirsutum and G.
mustelinum was constructed from a 59 individuals of BCv1Fv1 population. The map was
highly collinear with the G. hirsutum – G. barbadense map and the G. hirsutum
reference genome. In certain chromosomes, some markers exhibited segregation
distortion. Co-segregation difference between genetic maps revealed possible
chromosomal structure changes among species. Possible errors in the genome assembly
were found by alignments of 1,996 low-specificity SNP markers to their homeologs in
the reference genome. The genetic map can help guide genome assembly corrections,
and facilitate many sorts of future studies, e.g., genetic dissection of complex traits and
marker-assisted breeding.
Subject
CottonGossypium hirsutum
Gossypium mustelinum
Interspecific hybridization
Single-nucleotide polymorphism
Cotton63k array
Chromosome substitution lines
Recombinant inbred lines
Quantitative traits locus analysis
Fiber quality
Fusarium oxysporum f. sp. vasinfectum Race 4
Genetic background variance
Genetic mapping analysis
Citation
Lin, Yu-Ming (2017). High-Density SNP Genotyping Applied to Interspecific Germplasm in Upland Cotton (Gossypium Hirsutum L.): (I.) CSB17 Chromosome-Specific RIL Analysis and (II.) G. Mustelinum (Miers Ex Watt) Linkage Mapping. Master's thesis, Texas A & M University. Available electronically from https : / /hdl .handle .net /1969 .1 /173253.