Key message
A high-resolution GWAS detected consistent QTL for resistance to Verticillium wilt and Fusarium wilt race 4 in 376 U.S. Upland cotton accessions based on six independent replicated ...greenhouse tests.
Verticillium wilt (VW, caused by
Verticillium dahliae
Kleb.) and Fusarium wilt (FOV, caused by
Fusarium oxysporum
f.sp.
vasinfectum
Atk. Sny & Hans) are the most important soil-borne fungal diseases in cotton. To augment and refine resistance quantitative trait loci (QTL), we conducted a genome-wide association study (GWAS) using high-density genotyping with the CottonSNP63K array. Resistance of 376 US Upland cotton accessions to a defoliating VW and virulent FOV4 was evaluated in four and two independent replicated greenhouse tests, respectively. A total of 15 and 13 QTL for VW and FOV4 resistances were anchored by 30 (on five chromosomes) and 56 (on six chromosomes) significant single nucleotide polymorphic (SNPs) markers, respectively. QTL on c8, c10, c16, and c21 were consistent in two or more tests for VW resistance, while two QTL on c8 and c14 were consistent for FOV4 resistance in two tests. Two QTL clusters on c16 and c19 were observed for both VW and FOV4 resistance, suggesting that these genomic regions may harbor genes in response to both diseases. Using BLAST search against the sequenced TM-1 genome, 30 and 35 candidate genes were identified on four QTL for VW resistance and on three QTL for FOV4 resistance, respectively. These genomic regions were rich in NBS-LRR genes presented in clusters. The results create opportunities for further studies to determine the correlations of field resistance with these QTL, molecular examinations of VW and FOV4 resistances, marker-assisted selection (MAS) and eventual cloning of QTL for disease resistance in cotton.
Improving fiber quality and yield are the primary research objectives in cotton breeding for enhancing the economic viability and sustainability of Upland cotton production. Identifying the ...quantitative trait loci (QTL) for fiber quality and yield traits using the high-density SNP-based genetic maps allows for bridging genomics with cotton breeding through marker assisted and genomic selection. In this study, a recombinant inbred line (RIL) population, derived from cross between two parental accessions, which represent broad allele diversity in Upland cotton, was used to construct high-density SNP-based linkage maps and to map the QTLs controlling important cotton traits.
Molecular genetic mapping using RIL population produced a genetic map of 3129 SNPs, mapped at a density of 1.41 cM. Genetic maps of the individual chromosomes showed good collinearity with the sequence based physical map. A total of 106 QTLs were identified which included 59 QTLs for six fiber quality traits, 38 QTLs for four yield traits and 9 QTLs for two morphological traits. Sub-genome wide, 57 QTLs were mapped in A sub-genome and 49 were mapped in D sub-genome. More than 75% of the QTLs with favorable alleles were contributed by the parental accession NC05AZ06. Forty-six mapped QTLs each explained more than 10% of the phenotypic variation. Further, we identified 21 QTL clusters where 12 QTL clusters were mapped in the A sub-genome and 9 were mapped in the D sub-genome. Candidate gene analyses of the 11 stable QTL harboring genomic regions identified 19 putative genes which had functional role in cotton fiber development.
We constructed a high-density genetic map of SNPs in Upland cotton. Collinearity between genetic and physical maps indicated no major structural changes in the genetic mapping populations. Most traits showed high broad-sense heritability. One hundred and six QTLs were identified for the fiber quality, yield and morphological traits. Majority of the QTLs with favorable alleles were contributed by improved parental accession. More than 70% of the mapped QTLs shared the similar map position with previously reported QTLs which suggest the genetic relatedness of Upland cotton germplasm. Identification of QTL clusters could explain the correlation among some fiber quality traits in cotton. Stable and major QTLs and QTL clusters of traits identified in the current study could be the targets for map-based cloning and marker assisted selection (MAS) in cotton breeding. The genomic region on D12 containing the major stable QTLs for micronaire, fiber strength and lint percentage could be potential targets for MAS and gene cloning of fiber quality traits in cotton.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Bacterial blight (BB), caused by
Xanthomonas citri
pv.
malvacearum
(Xcm), is a destructive disease to cotton production in many countries. In the U.S., Xcm race 18 is the most virulent and ...widespread race and can cause serious yield losses. Planting BB-resistant cotton cultivars is the most effective method of controlling this disease. In this study, 335 U.S. Upland cotton accessions were evaluated for resistance to race 18 using artificial inoculations by scratching cotyledons on an individual plant basis in a greenhouse. The analysis of variance detected significant genotypic variation in disease incidence, and 50 accessions were resistant including 38 lines with no symptoms on either cotyledons or true leaves. Many of the resistant lines were developed in the MAR (multi-adversity resistance) breeding program at Texas A&M University, whereas others were developed before race 18 was first reported in the U.S. in 1973, suggesting a broad base of resistance to race 18. A genome-wide association study (GWAS) based on 26,301 single nucleotide polymorphic (SNP) markers detected 11 quantitative trait loci (QTL) anchored by 79 SNPs, including three QTL on each of the three chromosomes A01, A05 and D02, and one QTL on each of D08 and D10. This study has identified a set of obsolete Upland germplasm with resistance to race 18 and specific chromosomal regions delineated by SNPs for resistance. The results will assist in breeding cotton for BB resistance and facilitate further genomic studies in fine mapping resistance genes to enhance the understanding of the genetic basis of BB resistance in cotton.
Current morphometric methods that comprehensively measure shape cannot compare the disparate leaf shapes found in seed plants and are sensitive to processing artifacts. We explore the use of ...persistent homology, a topological method applied as a filtration across simplicial complexes (or more simply, a method to measure topological features of spaces across different spatial resolutions), to overcome these limitations. The described method isolates subsets of shape features and measures the spatial relationship of neighboring pixel densities in a shape. We apply the method to the analysis of 182,707 leaves, both published and unpublished, representing 141 plant families collected from 75 sites throughout the world. By measuring leaves from throughout the seed plants using persistent homology, a defined morphospace comparing all leaves is demarcated. Clear differences in shape between major phylogenetic groups are detected and estimates of leaf shape diversity within plant families are made. The approach predicts plant family above chance. The application of a persistent homology method, using topological features, to measure leaf shape allows for a unified morphometric framework to measure plant form, including shapes, textures, patterns, and branching architectures.
In its natural state, cotton (Gossypium spp.) is a perennial that flowers only under short‐day conditions. Early selection efforts eliminated this photoperiod requirement, allowing cotton cultivation ...to shift predominantly to annual growth under long summer daylengths throughout the world. Photoperiod sensitivity persists in many wild cottons and remains a major barrier to the introgression of beneficial alleles into elite breeding material. Identification of the variation and genetic factors underlying photoperiod response in cotton is needed to fully harness the genetic diversity of wild cotton and broaden the cultivated germplasm pool. Genetic variants, especially loss‐of‐function mutations in dominant genes conferring photoperiod sensitivity, would be highly valuable in this regard. After mutagenizing pima cotton (G. barbadense L.) seeds heterozygous for the major photoperiod response gene Gb_Ppd1 with γ rays, we identified plants no longer sensitive to photoperiod. Genetic analysis of BC1F1 plants derived from backcrossing the mutants with their photoperiod‐insensitive parent confirmed the loss‐of‐function mutations were allelic with Gb_Ppd1. Characterization of the mutants with molecular markers confirmed that all but one were deletions of Gb_Ppd1. Further, genotyping localized Gb_Ppd1 to a 12‐Mb region on chromosome D10. The newly identified genomic region and loss‐of‐function mutants may help assist with the identification and functional validation of candidate genes for photoperiod response in cotton, facilitating the valuable introgression of genetic diversity into cotton breeding programs.
Cotton grown in the United States are day‐length insensitive annuals and are grown under long‐day summers. Photoperiod sensitivity, present in tropical wild and landraces endemic to the center of ...origin and diversity, is a major barrier for the introgression of tropical gene pool into the US cotton. Previously, we mapped the major photoperiod response locus Gb_Ppd1 on chromosome D06 of Pima cotton (Gossypium barbadense L.). In the current study, an F2 population of 2112 gametes was used to fine map the Gb_Ppd1 locus. Two sequence‐tagged‐site and nine kompetitive allele‐specific polymerase chain reaction (KASP) markers were developed and the Gb_Ppd1 locus was fine mapped to 1.1 cM region flanked by novel markers 17‐KASP‐8, 17‐KASP‐10, and 15‐PR‐10A. The closely linked markers identified 2.10 Mb region in the G. barbadense genome that contained 18 putative gene sequences. A candidate gene Gbar_D06G014560 showed high homology to VASCULAR PLANT ONE ZINC FINGER PROTEIN 1 involved in photoperiodism in Arabidopsis. We evaluated the diagnostic polymorphisms for the flanking markers on a diversity panel of 91 Pima accessions. These markers would be useful in marker‐assisted selection of photoperiod response in cotton breeding. Further, quantitative gene expression analysis indicated that the CONSTANS (CO)/FLOWERING LOCUS T (FT) system is conserved in the photoperiod response pathway in Pima cotton, while CO and FT are likely not the causal genes underlying flowering time at the Gb_Ppd1 locus. The Gb_Ppd1 gene may be an upstream regulatory sequence in the FT gene pathway that controls photoperiodism in photoperiod‐sensitive cotton by affecting the CO/FT interaction under long‐day‐length conditions.
Core Ideas
The major effect photoperiod response locus (Gb_Ppd1) of Pima cotton was fine mapped to a 1.1 cM region flanked by new markers 15‐PR‐10A and 17‐KASP‐10.
Targeted genomic mapping of Gb_Ppd1 locus identified 18 putative genes in 2.10 Mb region of Gossypium barbadense genome.
Candidate gene analyses identified a homolog of VASCULAR PLANT ONE ZINC FINGER PROTEIN 1 as a candidate gene for Gb_Ppd1 locus.
Quantitative expression analysis indicated that the CO/FT system in the photoperiod response pathway is likely conserved in Pima cotton, while CO is likely not the causal gene at the Gb_Ppd1 locus.
ABSTRACT
Photoperiod sensitivity is a major barrier to using introgressions from the tropical gene pool in cotton breeding programs in North America. To better understand the genetic processes ...underlying photoperiod response in Pima cotton, a photoperiod‐insensitive line, Pima S‐7, was crossed to a photoperiod‐sensitive landrace accession, NC7018. An F2 mapping population of 211 individuals was used to establish that a single dominant gene controls the photoperiod sensitivity in Gossypium barbadense. Molecular mapping with simple sequence repeat (SSR) markers localized the photoperiod response gene Gb_Ppd1 to a 3.3‐cM region on chromosome 25 of the Pima cotton genetic map. Orthologous mapping of the flanking markers with the draft diploid D‐genome sequence resolved the photoperiod response gene to a 5.8 Mb region close to the centromere on chromosome 10 of Gossypium raimondii. In silico mapping of the flowering‐time candidate genes of model plant species suggested that the putative gene Gorai.010G161200 of G. raimondii, which has a function involved in photoperiodism, was mapped in the genomic region of Gb_Ppd1. Identification of closely linked molecular markers and the delineated genomic region in sequenced G. raimondii genome will aid marker‐assisted selection and molecular isolation of photoperiod response loci in cotton.
Improving fiber quality and yield are major research objectives for cotton breeders in the United States. Identifying broadly existing and stable quantitative trait loci (QTLs) related to fiber ...quality is critical to properly utilizing genomic resources in cotton improvement programs. An F6 recombinant inbred line (RIL) population derived from the cross of NC05AZ21 × TX‐2324 was used to develop linkage maps and for QTL analysis of six fiber quality traits and lint percentage. The Illumina 63K single nucleotide polymorphism (SNP) array was used to genotype the RIL population. Analysis of variance of phenotypic trait data showed significant differences among lines and years for all traits tested. The heritability for tested traits ranged from 0.56 to 0.91. Genetic mapping was performed using 3,009 polymorphic SNP markers on the RILs. We constructed a genetic map with a total length of 4,983.73 cM and an average distance of 1.66 cM between markers. The linkage map corresponded well with the Upland cotton (Gossypium hirsutum L.) sequence‐based physical map. Thirty‐two QTLs with additive effects for lint percentage and fiber quality traits were identified on 15 chromosomes, explaining 7.9–22.2% of the phenotypic variance. The majority of these QTLs were mapped in the D subgenome, indicating that functional mutations in the D subgenome are responsible for the major fiber quality improvements in Upland cotton. Furthermore, five QTL clusters were located on four chromosomes (Chr.05, Chr.18, Chr.19, and Chr.26), which may explain the strong correlation between fiber quality traits measured. The QTLs identified in the current study could be targeted for marker‐assisted selection and map‐based cloning of fiber quality traits in Upland cotton.
Core Ideas
QTL mapping using a SNP array on a recombinant inbred line population was performed.
The genetic map of SNPs corresponded well with the sequence‐based physical map.
Thirty‐two QTLs for six fiber quality traits and lint percentage were identified.
The D subgenome harbored the majority of QTLs for fiber quality in Upland cotton.
QTLs for fiber quality traits clustered on a handful of chromosomal regions.
In this study, genetic diversity and population structure was assessed in a set of 185 Gossypium hirsutum L. landrace accessions, collected mainly from Central America during the mid‐1900s using ...genomewide simple sequence repeat (SSR) markers. Genotyping the diversity panel using 122 SSRs detected 143 marker loci. A total of 819 alleles were identified across 143 markers loci, and out of these, 23.3% were unique alleles, observed only in one accession. Average genetic distance between accessions was 0.36, suggesting higher levels of genetic variation present in the cotton tropical landrace germplasm. Using Bayesian model‐based structure analysis, five major subgroups were identified that roughly corresponded to the geographical origins of accessions. Substantial admixture was observed as accessions from different geographical locations were grouped together. Results from phylogenetic analysis, principal component analysis, and analysis of molecular variance supported clustering based on STRUCTURE analysis. Pairwise kinship estimates suggested that most of the accessions were unrelated. Finally, core sets representing various levels of allelic richness were identified using POWERMARKER. Assessing genetic diversity, population structure, and identifying the core sets in the landraces will facilitate the utilization of unexploited tropical genetic diversity towards developing improved cotton cultivars.
•Significant variation in tolerance to drought and salt and resistance to thrips were observed within a diversity panel of 376 US Upland cotton•GWAS identified 11 and 15 common QTL between tests for ...drought and salt tolerance, respectively.•Eight QTL were identified for thrips resistance on five chromosomes.•Thirteen QTL clusters were detected on 11 chromosomes. Among the 13 QTL clusters, the one on D03 contained a QTL for thrips resistance and four QTL for abiotic resistance.
Upland cotton (Gossypium hirsutum L.) is the most important fiber-producing crop, and its seedlings are sensitive to abiotic and biotic stresses including drought, salt and thrips Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae). In this study, an association mapping panel of 376 Upland cotton accessions was evaluated to identify quantitative trait loci (QTL) for thrips resistance in two replicated tests and drought (DT) and salt tolerance (ST) each in three replicated tests. Significant genotypic differences were detected for severity rating-based thrips resistance and morphological traits (including plant height, fresh shoot weight, fresh root weight, dry shoot weight and dry root weight (except for ST), and physiological traits (including chlorophyll content reading, stomatal conductance, photosynthesis rate, transpiration, and leaf temperature) under DT and ST conditions. Heritability estimates were low for physiological traits, moderate for morphological traits measured for both DT and ST and moderate to high for thrips resistance. Based on a genome-wide association study (GWAS) using 26,301 polymorphic SNPs, 53 and 78 QTL were detected for DT and ST, respectively, on all 26 chromosomes except for A02, A04, A06, A12 and D07. Eleven and 15 QTL were common between tests for DT and ST, respectively. Twenty-three of 131 QTL were common between DT and ST. Eight QTL were identified for thrips resistance on five chromosomes (A09, D01, D02, D03 and D11). Thirteen QTL clusters were detected on 11 chromosomes (i.e., A01, A08, D01, D02, D03, D05, D06, D10, D11, D12, and D13). Among the 13 QTL clusters, the one on D03 contained a QTL for thrips resistance and four QTL for abiotic resistance. This study represented the first attempt to map thrips resistance QTL in cotton, providing important information for biotic and abiotic stress resistance to select QTL that will be useful for marker-assisted selection (MAS) in cotton.
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