Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.)

Key message

Genetic diversity and population structure in the US Upland cotton was established and core sets of allelic richness were identified for developing association mapping populations in cotton.

Abstract

Elite plant breeding programs could likely benefit from the unexploited standing genetic variation of obsolete cultivars without the yield drag typically associated with wild accessions. A set of 381 accessions comprising 378 Upland (Gossypium hirsutum L.) and 3 G. barbadense L. accessions of the United States cotton belt were genotyped using 120 genome-wide SSR markers to establish the genetic diversity and population structure in tetraploid cotton. These accessions represent more than 100 years of Upland cotton breeding in the United States. Genetic diversity analysis identified a total of 546 alleles across 141 marker loci. Twenty-two percent of the alleles in Upland accessions were unique, specific to a single accession. Population structure analysis revealed extensive admixture and identified five subgroups corresponding to Southeastern, Midsouth, Southwest, and Western zones of cotton growing areas in the United States, with the three accessions of G. barbadense forming a separate cluster. Phylogenetic analysis supported the subgroups identified by STRUCTURE. Average genetic distance between G. hirsutum accessions was 0.195 indicating low levels of genetic diversity in Upland cotton germplasm pool. The results from both population structure and phylogenetic analysis were in agreement with pedigree information, although there were a few exceptions. Further, core sets of different sizes representing different levels of allelic richness in Upland cotton were identified. Establishment of genetic diversity, population structure, and identification of core sets from this study could be useful for genetic and genomic analysis and systematic utilization of the standing genetic variation in Upland cotton.     

Measuring gene flow in the cultivation of transgenic cotton (Gossypium hirsutum L.)

Transgenic Bt cotton NewCott 33B and transgenic tfd A cotton TFD were chosen to evaluate pollen dispersal frequency and distance of transgenic cotton (Gossypium hirsutum L.) in the Huanghe Valley Cotton-producing Zone, China. The objective was to evaluate the efficacy of biosafety procedures used to reduce pollen movement. A field test plot of transgenic cotton (6×6 m) was planted in the middle of a nontransgenic field measuring 210×210 m. The results indicated that the pollen of Bt cotton or tfd A cotton could be dispersed into the environment. Out-crossing was highest within the central test plot where progeny from nontransgenic plants, immediately adjacent to transgenic plants, had resistant plant progeny at frequencies up to 10.48%. Dispersal frequency decreased significantly and exponentially as dispersal distance increased. The flow frequency and distance of tfd A and Bt genes were similar, but the pollen-mediated gene flow of tfd A cotton was higher and further to the transgenic block than that of Bt cotton (χ² = 11.712, 1 degree of freedom, p<0.001). For the tfd A gene, out-crossing ranged from 10.13% at 1 m to 0.04% at 50 m from the transgenic plants. For the Bt gene, out-crossing ranged from 8.16% at 1 m to 0.08% at 20 m from the transgenic plants. These data were fit to a power curve model: y=10.1321x ^−1.4133 with a correlation coefficient of 0.999, and y=8.0031x ^−1.483 with a correlation coefficient of 0.998, respectively. In this experiment, the farthest distance of pollen dispersal from transgenic cotton was 50 m. These results indicate that a 60-m buffer zone would serve to limit dispersal of transgenic pollen from small-scale field tests.     

Alternative approach for consistent yields of total genomic DNA from cotton (Gossypium hirsutum L.)

A persistent limitation to molecular biological research on cotton (Gossypium spp.) has been the difficulty in isolation of total genomic DNA from the plant tissue. This report describes a reliable strategy for isolation of genomic DNA from cotton. The mini-preparation procedure involves use of lyophilized, etiolated cotyledons and an anion exchange column kit. The isolated DNA had a molecular weight in excess of 50 kb with minimal degradation or shearing. Routine yields ranged from 5 to 7 μg DNA per etiolated cotyledon pair (corresponding to 100 ng/mg dry weight), in contrast to little or no DNA from equivalent amounts of either green cotyledons or mature leaf tissue. The decreased yields from the latter tissues appeared to be correlated with increased afmounts of flavonoid. The DNA was amenable to routine molecular applications as demonstrated by: digestibility with a number of restriction enzymes (Eco RI,HindIII,Sau 3A), and hybridization of a tomato genomic clone containing the gene for S-adenosylmethionine synthetase to a 13.3-kbEco RI fragment of cotton. Using DNA from an isoline immune to root-knot nematodes, we observed no impediment to genomic cloning.     

Infraspecific DNA methylation polymorphism in cotton (Gossypium hirsutum L.)

Cytosine methylation is important in the epigenetic regulation of gene expression and development in plants and has been implicated in silencing duplicate genes after polyploid formation in several plant groups. Relatively little information exists, however, on levels and patterns of methylation polymorphism (MP) at homologous loci within species. Here we explored the levels and patterns of methylation-polymorphism diversity at CCGG sites within allotetraploid cotton, Gossypium hirsutum, using a methylation-sensitive amplified fragment length polymorphism screen and a selected set of 20 G. hirsutum accessions for which we have information on genetic polymorphism levels and relationships. Methylation and MP exist at high levels within G. hirsutum: of 150 HpaII/MspI sites surveyed, 48 were methylated at the inner cytosine (32%) and 32 of these were polymorphic (67%). Both these values are higher than comparable measures of genetic diversity using restriction fragment length polymorphisms. The high percentage of methylation-polymorphic sites and potential relationship to gene expression underscore the potential significance of MP within and among populations. We speculate that biased correlation of methylation-polymorphic sites and genes in cotton may be a consequence of polyploidy and the attendant doubling of all genes.     

Water-deficit stress effects on pistil biochemistry and leaf physiology in cotton (Gossypium hirsutum,L.)

Flowering in cotton (Gossypium hirsutum L.) is a sensitive stage to water-deficit stress, but the effects on metabolism are not well understood. The objective of this study was to monitor gas exchange responses of cotton plants under conditions of limited water supply and evaluate the effects on the carbohydrate concentrations and glutathione reductase levels in the cotton flower. Growth chamber experiments were conducted in 2008 and 2009, with normal day/night conditions of 32/24 °C and optimum quantities of Hoagland's nutrient solution applied until flowering. Treatments were imposed at flowering and consisted of control (Control), where optimum quantities of water were applied, and water stress (WS) where 50% of optimum quantity of water was supplied. Water-deficit stress resulted in a significant decrease in leaf stomatal conductance. Leaf photosynthetic and respiration rates were similarly decreased compared to the control. Ovary and style water potential of water-stressed leaves were significantly higher compared to the water potential of water stressed leaves, indicating that cotton flowers are fairly resistant to changes in the water status of the plant. However, carbohydrate concentrations of water-stressed pistils (ovary and style) were significantly increased compared to the control and a similar pattern was observed in the levels of glutathione reductase of water-stressed pistils. In conclusion, water-deficit stress during flowering resulted in significant decreases in leaf gas exchange functions as well as leaf water potential. Cotton pistils appeared to be less sensitive since they were able to maintain water potential similar to the control under limited water supply and increase glutathione reductase levels. However, pistil carbohydrate metabolism was significantly affected resulting in accumulation of both hexose and sucrose indicating a perturbation in sucrose cleaving and hexose utilizing enzymes that could potentially have as a consequence a decrease in fertilization and seed set efficiency.     

Somatic embryogenesis and plant regeneration in cotton (Gossypium hirsutum L.)

Tissue culture methods for improvement of cotton has lagged seriously compared to other major crops. A method for regeneration of cotton which includes a morphogenetically competent cell suspension was needed to facilitate selection of stress-resistant variants and gene manipulation. Preliminary screening of eight strains of Gossypium hirsutum L. for embryogenic potential resulted in the production of somatic embryos in all strains. Coker 312 was selected for use in the development of a model regeneration system for G. hirsutum. Calli were initiated from hypocotyl tissues of 3-day-old-seedlings. Globular embryos were present after six weeks in culture. Calli were subcultured to liquid suspension in growth regulator-free medium. After three to four weeks, suspensions were sieved to collect globular and heart stage embryos. Collected embryos developed further when plated onto semi-solid medium. To induce germination and plantlet growth, mature embryos were placed on sterile vermiculite saturated with medium. Upon development of roots and two true leaves, plantlets were potted in peat and sand, and hardened. Mature plants and progeny have been obtained with this procedure. A high percentage of infertile plants was observed among the regenerants.Abbreviations NAA 1 naphthaleneacetic acid - IAA indole-3-acetic acid - 2,4-D 2,4-dichlorophenoxyacetic acid - GA₃ gibberellic acid - MS Murashige and Skoog - BA 6 benzylamino purine - 2i P N⁶-(²-isopentenyladenine     

Transformation of cotton (Gossypium hirsutum L.) via particle bombardment

Embryogenic suspension cultures of cotton (Gossypium hirsutum L.) were subjected to particle bombardment, where high density particles carrying plasmid DNA were accelerated towards the embryogenic plant cells. The plasmid DNA coating the particles encoded hygromycin resistance. One to two weeks following bombardment, embryogenic cotton cells were placed in proliferation medium containing 100 g/ml hygromycin. Clumps of tissue which grew in the presence of hygromycin were subcultured at low density into fresh hygromycin-containing proliferation medium. Following sequential transfer of embryogenic tissue to development and then germination media, plants were recovered from transgenic embryogenic tissue. Southern hybridization confirmed the presence of the hygromycin resistance gene in embryogenic suspension culture tissue and regenerated plants.Abbreviations 2,4-D 2,4-dichlorophenoxyacetic acid - GUS -glucuronidase - Aph IV aminoglycoside phosphotransferase type IV Salaries and research support were provided by State and Federal funds appropriated to OSU/OARDC and USDA-ARS. Mention of trademark or proprietary products does not constitute a guarantee or warranty of the product by OSU/OARDC or USDA, and also does not imply approval to the exclusion of other products that may also be suitable. Journal Article No. 354-89     

Rapid in-vitro plant regeneration of cotton (Gossypium hirsutum L.)

A rapid, clonal propagation procedure has been developed to regenerate mature cotton (Gossypium hirsutum L.) plants from pre-existing meristems that were excised from in-vitro-grown tissues. This plant regeneration procedure was applicable to diverse cotton germplasms and required specific concentrations of 6-benzylaminopurine (BA) depending on the origin of the meristems. All shoots regenerated directly without a callus phase. Screening BA concentrations (0.0–10.0 μm) demonstrated that shoot meristems (apices), secondary leaf nodes, primary leaf nodes, and cotyledonary nodes derived from in-vitro-grown 28-day-old seedlings (Paymaster HS26) varied in their ability to form elongated shoots depending on the level of BA. Indicative of a germplasm-independent procedure, a BA concentration screen (0.0, 0.3, 1.0 μm) demonstrated that explants with pre-existing meristems, excised from diverse germlines, were also able to form elongated shoots at 0.3 μm BA. In most cases, elongated shoots derived from this procedure were rooted by a two-step process: an in-vitro maturation step (Murashige and Skoog medium-activated charcoal) followed by planting into soil after basal application of Rootone. This BA plant regeneration procedure was rapid, reproducible, and highly efficient for Stoneville 7A, Paymaster HS26, and other high-fiber-yielding germlines. Regenerated plants were phenotypically normal and all of the mature plants regenerated to date have initiated flowers and set viable R₁ seeds. Received: 15 March 1997 / Revision received: 28 August 1997 / Accepted: 5 September 1997     

A study of heterosis in upland cotton (Gossypium hirsutum L.)

Summary Heterosis (over mid parent) and useful heterosis (over commercial variety H14) estimates were obtained from a line x tester analysis of crosses involving thirteen diverse female parents with two locally adapted varieties H14 (local standard) and J34. Marked heterosis was observed for seed cotton yield, boll number and halo length. The values of positive heterosis and useful heterosis for seed cotton yield ranged from 28.1 to 87.0% and 20.1 to 45.5%, respectively. The overall study of heterosis revealed that female parents PRS-72 (USSR), 5904F (USSR) and MCU-5 (Madras Cambodian Uganda Selection, Coimbatore) were among the top three females, showing considerable heterosis in crosses with H14 and J34 for seed cotton yield and fibre properties. The practical difficulties in exploiting the phenomenon of heterosis and possible experimental approaches in upland cotton are discussed.     

Breeding for reduced seed coat fuzz in Upland cotton (Gossypium hirsutum)

The inheritance of seed coat fuzz was studied in two half diallel sets of crosses of Upland cotton. One with F₄ selections from an inter-varietal cross showed a significant level of non-additive variance attributable to dominance and non-allelic interaction. In the other, using inbred varieties of diverse origin, the genetic control of seed fuzz was adequately accounted for by an additive-dominance model with no interaction. Genotypic correlations between seed coat fuzz, yield and lint quality characters, calculated for both diallel sets and for two other groups of breeding material, showed good agreement within each experiment between parents and hybrids or between parents and progenies but no consistent pattern between experiments. The results serve to emphasize the risks in extrapolating correlations from one group of breeding material to another. A useful level of reduced fuzz has been obtained in selections from the AH breeding programme and the genetical investigations indicate that a further reduction may be possible, thereby leading to easier handling of seed, speedier and cheaper ginning, low levels of seed coat nep and better seed germination.     

An RFLP linkage map of Upland cotton, Gossypium hirsutum L.

 Ninety-six F₂.F₃ bulked sampled plots of Upland cotton, Gossypium hirsutum L., from the cross of HS46×MARCABUCAG8US-1-88, were analyzed with 129 probe/enzyme combinations resulting in 138 RFLP loci. Of the 84 loci that segregated as co-dominant, 76 of these fit a normal 1 :  2 : 1 ratio (non-significant chi square at P=0.05). Of the 54 loci that segregated as dominant genotypes, 50 of these fit a normal 3: 1 ratio (non-significant chi square at P=0.05). These 138 loci were analyzed with the MAPMAKER∖ EXP program to determine linkage relationships among them. There were 120 loci arranged into 31 linkage groups. These covered 865 cM, or an estimated 18.6% of the cotton genome. The linkage groups ranged from two to ten loci each and ranged in size from 0.5 to 107 cM. Eighteen loci were not linked. Received: 31 March 1998 / Accepted: 29 April 1998     

Effects of fusicoccin on intact cotton plants (Gossypium hirsutum L.)

Fusicoccin (FC) was applied as a spray to shoots of intact field- and glasshouse-grown cotton plants. Distortions of shoot morphology resulted. Stems and petioles of FC-treated plants were irregular in diameter and twisted, whereas leaf laminae were curled and crinkled. Shoot elongation was inhibited by FC; the effect was dependent upon the concentration and timing of the applications.Abbreviation FC fusicoccin     

MicroRNA-target gene responses to root knot nematode (Meloidogyne incognita) infection in cotton (Gossypium hirsutum L.)

MicroRNAs (miRNAs) are a large class of small regulatory RNA molecules, however no study has been performed to elucidate the role of miRNAs in cotton (Gossypium hirsutum) response to the root knot nematode (RKN, Meloidogyne incognita) infection. We selected 28 miRNAs and 8 miRNA target genes to investigate the miRNA-target gene response to M. incognita infection. Our results show that RKN infection significantly affected the expression of several miRNAs and their targeted genes. After 10 days of RKN infection, expression fold changes on miRNA expressions ranged from down-regulated by 33% to upregulated by 406%; meanwhile the expression levels of miRNA target genes were 45.8% to 231%. Three miRNA-target pairs, miR159-MYB, miR319-TCP4 and miR167-ARF8, showed inverse expression patterns between gene targets and their corresponded miRNAs, suggesting miRNA-mediated gene regulation in cotton roots in response to RKN infection.     

Wide-cross whole-genome radiation hybrid mapping of cotton (Gossypium hirsutum L.)

We report the development and characterization of a "wide-cross whole-genome radiation hybrid" (WWRH) panel from cotton (Gossypium hirsutum L.). Chromosomes were segmented by gamma-irradiation of G. hirsutum (n = 26) pollen, and segmented chromosomes were rescued after in vivo fertilization of G. barbadense egg cells (n = 26). A 5-krad gamma-ray WWRH mapping panel (N = 93) was constructed and genotyped at 102 SSR loci. SSR marker retention frequencies were higher than those for animal systems and marker retention patterns were informative. Using the program RHMAP, 52 of 102 SSR markers were mapped into 16 syntenic groups. Linkage group 9 (LG 9) SSR markers BNL0625 and BNL2805 had been colocalized by linkage analysis, but their order was resolved by differential retention among WWRH plants. Two linkage groups, LG 13 and LG 9, were combined into one syntenic group, and the chromosome 1 linkage group marker BNL4053 was reassigned to chromosome 9. Analyses of cytogenetic stocks supported synteny of LG 9 and LG 13 and localized them to the short arm of chromosome 17. They also supported reassignment of marker BNL4053 to the long arm of chromosome 9. A WWRH map of the syntenic group composed of linkage groups 9 and 13 was constructed by maximum-likelihood analysis under the general retention model. The results demonstrate not only the feasibility of WWRH panel construction and mapping, but also complementarity to traditional linkage mapping and cytogenetic methods.     

Chronology of the differentiation of cotton (Gossypium hirsutum L.) fiber cells

Cotton fibers are single elongated cells that develop from epidermal cells of the ovule. The chronology of fiber differentiation was investigated using cultured ovules. Epidermal cells differentiate into fiber cells approx. 3 d before anthesis. When ovules were cultured on a defined medium, fiber growth could be initiated on ovules any time between 2 d preanthesis and the time of anthesis by adding indole-3-acetic acid and gibberellic acid to the medium. In the absence of phytohormones, fibers did not grow, and when ovules between 2 d preanthesis and anthesis were cultured without hormones past the day of anthesis and hormones then added, most ovules failed to produce fibers. The results define the timing of fiber differentiation from epidermal cells, and also define a window of time when differentiated cells are capable of further development. During this window, fiber cells are latent awaiting appropriate stimulation which in the intact plant is apparently associated with anthesis.Abbreviations GA₃ gibberellic acid - IAA indole-3-acetic acid     

陆地棉遗传图谱构建与纤维品质性状QTL定位

以陆地棉(Gossypium hirsutum L.)品种Bar19/1和Acala1517-77杂交的108个F2单株为材料,应用85个标记(70个SSR标记和15个AFLP标记)构建了总长为814cM的遗传图谱,覆盖棉花基因组的18.3%。该图谱包含25个连锁群,分别对应到17条染色体和4个未知连锁群。应用复合区间作图法分析了该组合的108个F2单株和F3家系纤维品质性状,从遗传图谱上检测到19个纤维品质数量性状基因座(QTL),包括5个纤维长度、6个纤维比强度、4个伸长率及4个马克隆值QTL,分别解释各性状表型变异的15.11%~28.45%、8.46%~24.51%、11.08%~27.55%和9.23%~42.21%。纤维长度和伸长率的QTL以部分显性为主,少数具有超显性,比强度QTL以加性和部分显性为主,4个马克隆值QTL中有3个表现为超显性。研究结果表明,陆地棉Bar19/1和Acala1517-77间多态性位点丰富,有利于构建高密度遗传图谱,纤维品质性状的QTL分析从分子水平上揭示了纤维品质的遗传基础。     

Chilling injury in cotton (Gossypium hirsutum L.) Prevention by abscisic acid

Cotton (Gossypium hirsutum L.) intact seedlings and isolatedcotyledonary discs were exposed to chilling (4?C) under humidconditions which prevented dehydration. The damage resultingfrom chilling was estimated by means of electrolyte leakageand survival in whole seedlings and by the electrolyte leakageand necrotic areas in isolated cotyledonary discs. Also, theeffect of chilling on membrane phospholipids and cellular reducedglutathione was determined. Within the first two and three daysof chilling, there was a marked reduction in the reduced glutathioneand membrane phospholipid levels without electrolyte loss andnecrosis. This reduction was completely prevented by pretreatmentwith abscisic acid. Prolonging the chilling period resultedin decreased survival in whole seedlings and in progressiveincrease in electrolyte leakage and necrosis in isolated cotyledonarydiscs. Pretreatment with abscisic acid prior to chilling almostcompletely prevented this chilling injury when exposure to 4?Cwas less than 5 days. Even with longer chilling periods, theabscisic acid pretreatment greatly reduced the damage. ³Incumbent of the Seagram Chair in Plant Science. (Received July 21, 1979; )