Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton (Gossypium hirsutum)

Cultivated cotton (Gossypium hirsutum) is the most important fibre crop in the world. Cotton leaf curl disease (CLCuD) is the major limiting factor and a threat to textile industry in India and Pakistan. All the local cotton cultivars exhibit moderate to no resistance against CLCuD. In this study, we evaluated an exotic cotton accession Mac7 as a resistance source to CLCuD by challenging it with viruliferous whiteflies and performing qPCR to evaluate the presence/absence and relative titre of CLCuD‐associated geminiviruses/betasatellites. The results indicated that replication of pathogenicity determinant betasatellite is significantly attenuated in Mac7 and probably responsible for resistance phenotype. Afterwards, to decipher the genetic basis of CLCuD resistance in Mac7, we performed RNA sequencing on CLCuD‐infested Mac7 and validated RNA‐Seq data with qPCR on 24 independent genes. We performed co‐expression network and pathway analysis for regulation of geminivirus/betasatellite‐interacting genes. We identified nine novel modules with 52 hubs of highly connected genes in network topology within the co‐expression network. Analysis of these hubs indicated the differential regulation of auxin stimulus and cellular localization pathways in response to CLCuD. We also analysed the differential regulation of geminivirus/betasatellite‐interacting genes in Mac7. We further performed the functional validation of selected candidate genes via virus‐induced gene silencing (VIGS). Finally, we evaluated the genomic context of resistance responsive genes and found that these genes are not specific to A or D sub‐genomes of G. hirsutum. These results have important implications in understanding CLCuD resistance mechanism and developing a durable resistance in cultivated cotton.     

Population genomics reveals a fine‐scale recombination landscape for genetic improvement of cotton

Recombination breaks up ancestral linkage disequilibrium, creates combinations of alleles, affects the efficiency of natural selection, and plays a major role in crop domestication and improvement. However, there is little knowledge regarding the variation in the population‐scaled recombination rate in cotton. We constructed recombination maps and characterized the difference in the genomic landscape of the population‐scaled recombination rate between Gossypium hirsutum and G. arboreum and sub‐genomes based on the 381 sequenced G. hirsutum and 215 G. arboreum accessions. Comparative genomics identified large structural variations and syntenic genes in the recombination regions, suggesting that recombination was related to structural variation and occurred preferentially in the distal chromosomal regions. Correlation analysis indicated that recombination was only slightly affected by geographical distribution and breeding period. A genome‐wide association study (GWAS) was performed with 15 agronomic traits using 267 cotton accessions and identified 163 quantitative trait loci (QTL) and an important candidate gene (Ghir_COL2) for early maturity traits. Comparative analysis of recombination and a GWAS revealed that the QTL of fibre quality traits tended to be more common in high‐recombination regions than were those of yield and early maturity traits. These results provide insights into the population‐scaled recombination landscape, suggesting that recombination contributed to the domestication and improvement of cotton, which provides a useful reference for studying recombination in other species.     

Compensation to simulated insect leaf herbivory in wild cotton (Gossypium hirsutum): responses to multiple levels of damage and associated traits

• Identifying the mechanisms of compensation to insect herbivory remains a major challenge in plant biology and evolutionary ecology. Most previous studies have addressed plant compensatory responses to one or two levels of insect herbivory, and the underlying traits mediating such responses remain elusive in many cases.
• We evaluated responses associated with compensation to multiple intensities of leaf damage (0% control, 10%, 25%, 50%, 75% of leaf area removed) by means of mechanical removal of foliar tissue and application of a caterpillar (Spodoptera exigua) oral secretions in 3‐month‐old wild cotton plants (Gossypium hirsutum). Four weeks post‐treatment, we measured plant growth and multiple traits associated with compensation, namely: changes in above‐ and belowground, biomass and the concentration of nutrients (nitrogen and phosphorus) and non‐structural carbon reserves (starch and soluble sugars) in roots, stems and leaves.
• We found that wild cotton fully compensated in terms of growth and biomass allocation when leaf damage was low (10%), whereas moderate (25%) to high leaf damage in some cases led to under‐compensation. Nonetheless, high levels of leaf removal (50% and 75%) in most cases did not cause further reductions in height and allocation to leaf and stem biomass relative to low and moderate damage. There were significant positive effects of leaf damage on P concentration in leaves and stems, but not roots, as well as a negative effect on soluble sugars in roots.
• These results indicate that wild cotton fully compensated for a low level of leaf damage but under‐compensated under moderate to high leaf damage, but can nonetheless sustain growth despite increasing losses to herbivory. Such responses were possibly mediated by a re‐allocation of carbohydrate reserves from roots to shoots.

     

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     

Characterization of somatic embryogenesis and plant regeneration in cotton (Gossypium hirsutum L.)

Summary Seventeen cultivars of cotton (Gossypium hirsutum L.) were evaluated for callus initiation and maintenance using 3 initiation media and 3 maintenance media. After a series of transfers of a 3% glucose media, calli were placed on a 3% sucrose medium. After several weeks calli were observed for the presence of embryo-like structures. Cultivars Coker 201 and Coker 315 were identified as embryogenic. Embryogenic callus has since been routinely obtained within 6 weeks by initiating callus on glucose media for 3–4 weeks followed by transfer to sucrose media. Histological examination has shown that embryos are derived from isodiametric, densely cytoplasmic cells and follow predictable patterns of development. Upon maturity, transfer to auxin-free media with reduced sucrose levels results in embryo germination. Regenerated plants can be transferred to greenhouse within 90 days of callus initiation.The senior author is presently a Research Geneticist, USDA-ARS, and Assistant Professor Present address     

A genetic approach to in vitro regeneration of non-regenerating cotton (Gossypium hirsutum L.) cultivars

Selections were made among individual plants of Gossypium hirsutum cv `Coker 310' for high-frequency in vitro regeneration by somatic embryogenesis. After three generations of selection, a pure line for high-frequency somatic embryogenesis was selected and named Coker 310 FR (FR, fully regenerating). Coker 310 FR could be regenerated by following previously published protocols (see Materials and methods) and a modified protocol developed in this study that reduced the time necessary for in vitro regeneration. Coker 310 FR was crossed with individual plants of major cotton cultivars grown in India, namely `MCU 5', `MCU 7', `Khandwa 2', `Bikaneri Nerma', `F 846' that have been shown to be recalcitrant to in vitro regeneration, to evaluate the regeneration potential of F₁s. All the F₁s showed regeneration by somatic embryogenesis. However, the F₁ of G. barbadense×G. hirsutum Coker 310 FR did not regenerate. Received: 16 September 1997 / Revision received: 1 April 1998 / Accepted: 15 May 1998     

Storage protein accumulation patterns in somatic embryos of cotton (Gossypium hirsutum L.)

Summary The storage protein content of somatic embryos of Gossypium hirsutum L. cv. Coker 201 was determined using extinction level, antigen/antibody association detection methods. Mature storage protein was first detected in early globular-stage somatic embryos at a total concentration of 0.36% of the embryo protein mass. Tulip-stage and mature somatic embryos were comprised of 3.0% and 1.3% mature storage protein, respectively. Maximum storage protein synthesis was found to occur during early globular- and early heart-stages. During this period of development, significant levels of protein precursors were found also to accumulate. The pattern of storage protein synthesis, processing and accumulation paralleled the pattern that has been reported for the zygotic system, although somatic embryos accumulate storage protein at much earlier stages and to a lesser degree. The possibility of using complex biochemical pathways to monitor embryogenic systems in vitro is discussed.     

Correlation studies on yield and fibre traits in upland cotton (Gossypium hirsutum L.)

Summary Two diverse parents of upland cotton namely J.34 and I.C. 1926 were crossed. A comparison between biparental intermated progenies and F₃ families indicated alteration of correlation coefficient between yield and halo length. The significant negative correlation in F₃ population between these two attributes changed to a positive but non significant one in biparental intermated progenies. A change in correlation coefficients was expected due to breakage of linkage upon intermating. An increase in the correlation coefficients could also be expected when linkages are predominantly in the repulsion phase. It is suggested that intermating in early generations coupled with selection of desirable segregants may prove a useful method for improving yield and quality simultaneously. The diallel selective mating system may also supplement intermating to improve yield and quality in cotton.Part of Ph.D. Thesis submitted to the Haryana Agricultural University. Hissar-125004, India     

Line x tester analysis for fixed effect model in cotton (Gossypium hirsutum L.)

Summary The data from an experiment in cotton consisting of three testers and 12 lines selected deliberately have been analysed. The investigation showed higher specific combining ability variance for yield of seed cotton and number of bolls, indicating the predominance of non-additive gene action. Of parental lines, H777 was found to possess high g.c.a. effects for seed cotton yield, number of bolls and number of sympodes. Parent H842 contributed only for boll weight, whereas H655 was good general combiner for number of monopodes. There appeared to be better chances for increasing the yield by exploiting hybrid vigour for the number of bolls and boll weight. The presence of marked non-additive gene effects, in addition to additive gene effects, indicated the need for exploiting both the fixable and non-fixable components of genetic variance for increasing productivity in cotton.     

In vitro induction of multiple shoots and plant regeneration in cotton (Gossypium hirsutum L.)

Induction of multiple shoots in cotton (Gossypium hirsutum L. cv. Anjali-LRK 516) has been achieved with cotyledonary nodes devoid of cotyledons and apical meristems. Explants from 35-day-old seedlings yielded the maximum number of shoots (4.7 shoots/explant) using Murashige and Skoog (MS) basal medium supplemented with 6-benzylaminopurine and kinetin (2.5 mg/1 each). Explants from 35-day-old seedlings raised in glass bottles produced a higher number of multiple shoots (8.3 shoots/explant) than those grown in glass tubes and cultured on the same shoot induction medium. Elongation of multiple shoots was obtained on liquid or agar MS basal medium without phytohormones. In vitro shoots were rooted on half-strength agar-solidified MS basal medium or with 0.05 or 0.1 mg/1 naphthaleneacetic acid. Hardening and survival of tissue culture plantlets was 95% under greenhouse conditions.Abbreviations BAP 6-Benzylaminopurine - GA₃ Gibberellic acid - MS Murashige and Skoog medium - NAA -Napthaleneacetic acid     

Plant regeneration via somatic embryogenesis in many cultivars of cotton (Gossypium hirsutum L.)

Summary Embryogenic callus was formed from several cultivars of cotton (Gossypium hirsutum L.) when sections of hypocotyl and cotyledon were cultured on medium supplemented with 5 mg/liter 6-(γ, γ-dimethylallyl-amino)-purine (2iP) and 0.1 mg/liter α-naphthaleneacetic acid (NAA) for callus initiation and proliferation, and subcultured on medium supplemented with 5 mg/liter NAA and 0.1 to 1 mg/liter 2iP for embryogenic callus induction. It seems that a high 2iP:auxin ratio is preferred for callus initiation and proliferation, but should be exchanged with a higher NAA:cytokinin ratio before differentiation will occur. Embryogenic calluses were recovered at a frequency of 2 to 85% depending on the cultivar used. Coker cultivars produced embryogenic callus faster and at higher frequencies than other cultivars. Embryogenic callus produced somatic embryos on phytohormone-free medium. This medium was used to maintain and proliferate embryogenic callus for a perid of 18 to 24 mo. Somatic embryos were converted to plants on a lower ionic strength medium supplemented with 0.1 mg/liter gibberellic acid (GA₃) and 0.01 mg/liter NAA. Glucose was the only carbohydrate used through all phases of tissue culture and was much better than sucrose, on which phenolic production was very high. High temperature (30° C) and low light intensity (9 μE · m⁻² · s⁻¹) were optimal conditions for callus initiation, embryogenic callus induction, and maintenance, whereas lower temperature (25° C) and high light intensity (90 μE · m⁻² s⁻¹) were the optimal conditions for somatic embryo maturation, germination, and plantlet development. Plants could be regenerated within 10 to 12 wk in Cokers or 7 to 8 mo. in others.     

Maternal effects and generation mean analysis of seed-oil content in cotton (Gossypium hirsutum L.)

Summary The nature of gene action and of maternal influence governing cottonseed oil attributes were determined with four lines, two each with high and low seed-oil percentage. For this purpose, P1, P2, F0, F1, F2 and alternative sets of BC1 and BC2 generations were analysed in six cross-combinations and their reciprocals. Marginal extents of heterosis for seed-oil percentage were noticeable in F1, with inbreeding depression in F2. Data from reciprocal backcrosses provided evidence in favour of maternal rather than cytoplasmic effects of seed-oil development. Relatively higher extents of heterosis, sizeable inbreeding depression and reciprocally unequal F2 averages were characteristic of the seed index trait, which often showed a reversal of effects from F1 to F2. Reverse reciprocal backcrosses exhibited some differences, including greater resemblance between the types, (A/B)A and (B/A)A, in addition to variable dose effects in seed index. Thus, the differences between F1 seed index values were not due to cytoplasmic influence. Positive heterotic effects for seed-oil index, especially among the backcrosses, ranged between 16.08% and 47.29% over midparent averages. Genetic component estimates from analysis of similar sets of crosses differing only in reciprocal backcrosses, and also from sets of reciprocal crosses between any two parental combinations, were inconsistent. Scaling tests detected presence of epistasis within and between a majority of cross-combinations. Despite reciprocal differences, additive gene effects for seed-oil percentage were significant in 7 out of 24 crosses, representing high x low, low x high and low x low seed-oil parents. Those were, however, accompanied by significant dominance effects of higher order. In crosses involving low seed-oil percentage parents SA1060 and SA229, all six components were detected significant, with opposite effects of dominance and dominance x dominance epistatic components. Significant additive components were also detected for seed index and seed-oil index in 7 and 5 out of 24 crosses, respectively. In the inheritance of seed index and seed-oil index, dominance effects were more important. Epistatic components of additive x additive, and to a lesser extent, those of dominant x dominant were found significant.