Proteomics profiling of fiber development and domestication in upland cotton (Gossypium hirsutum L.).

Comparative proteomic analyses were performed to detail the evolutionary consequences of strong directional selection for enhanced fiber traits in modern upland cotton (Gossypium hirsutum L.). Using two complementary proteomic approaches, 2-DE and iTRAQ LC-MS/MS, fiber proteomes were examined for four representative stages of fiber development. Approximately 1,000 protein features were characterized using each strategy, collectively resulting in the identification and functional categorization of 1,223 proteins. Unequal contributions of homoeologous proteins were detected for over a third of the fiber proteome, but overall expression was balanced with respect to the genome-of-origin in the allopolyploid G. hirsutum. About 30% of the proteins were differentially expressed during fiber development within wild and domesticated cotton. Notably, domestication was accompanied by a doubling of protein developmental dynamics for the period between 10 and 20 days following pollination. Expression levels of 240 iTRAQ proteins and 293 2-DE spots were altered by domestication, collectively representing multiple cellular and metabolic processes, including metabolism, energy, protein synthesis and destination, defense and stress response. Analyses of homoeolog-specific expression indicate that duplicated gene products in cotton fibers can be differently regulated in response to selection. These results demonstrate the power of proteomics for the analysis of crop domestication and phenotypic evolution.

Genetic analysis and molecular validation of gene conferring petal spot phenotype in interspecific crosses of cotton.

Cotton (Gossypium species) has received considerable interest from the geneticists, cytologists and evolutionary biologists since the last more than a century. Here, we explore the genetics of petal spot in the interspecific derivatives involving tetraploid and diploid cottons; and confirm the location of gene governing petal spot phenotype on chromosome A7 by demonstrating co-segregation of SSR marker NAU 2186 with petal spot phenotype. The presence of petal spot was observed to be dominant over its absence. Petal spot inheritance showed significant deviation from the expected Mendelian ratio in all the segregating populations indicating segregation distortion. The distortion was biased towards the hirsutum parent which has important implications from introgression point of view. We also report a strong association between petal spot and petal margin coloration phenotypes. Extant American cotton varieties generally lack petal spot and margin coloration phenotypes. These petal characteristics can serve as morphological markers during germplasm characterization.

Identification of SSR markers through bulk segregant analysis and inheritance of resistance to yellow vein mosaic disease in okra (Abelmoschus esculentus L. Moench).

Okra is an important traditional vegetable crop grown for its tender fruits in various tropical and sub tropical parts of the world. Yellow Vein Mosaic Disease (YVMD) is the major biotic factor causing severe threat to the okra fruit yield and qualities. The present study was conducted to find out the inheritance of resistance against YVMD and to identify the disease linked molecular markers through bulk segregant analysis. For this, the F1, BC1F1 and BC1F2 generations were derived from a cross between Abelmoschus manihot (PAUAcc-1) as resistant male parent and A. esculentus cv. Punjab Padmini as susceptible female parent. The whole set of populations (F1, BC1F1 and BC1F2) along with parents were subjected to artificial as well as filed screening against YVMD. Chi-square test for goodness to fit revealed that resistance against YVMD is controlled by two recessive genes. The allele of at least one gene in homozygous state mask the effect of other gene and produce a resistant phenotype. The very low polymorphism (31.5%) was detected between the parents by using SSR primers. Out of 200 SSR primers, the four primers i.e. Okra 032, Okra 049, Okra 129 and Okra 270 were found to be linked to YVMD through bulk segregant analysis. The identified SSR primers to YVMD could be further used in okra improvement for YVMD resistance. Supplementary Information: The online version contains supplementary material available at 10.1007/s13337-023-00844-9.

Comparison of Mineral Composition in Microgreens and Mature leaves of Celery (Apium graveolens L.).

Celery (Apium graveolens L.), a medicinal crop, occupies a significant position in the human diet possessing several essential macro- and microelements. For proper proximate analysis, an experiment was executed by taking 20 celery genotypes. The genotypes were analyzed for macro- and microminerals which include nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), sodium (Na), sulfur (S), zinc (Zn), iron (Fe), copper (Cu), and manganese (Mn). Results from analysis revealed that the  amount of N, P, Ca, Na, and S was higher in microgreens, whereas a higher value for K was found in mature leaves. Zn, Cu, and Mn contents were found to be higher in mature leaves, while no significant difference was observed for Fe content in microgreens and mature leaves. The inclusion of celery microgreens in our daily diet would fulfill a significant portion of our daily mineral requirement. This is the first report on mineral comparison between microgreens and mature leaves of celery. It opens a new avenue for further enhancement of minerals via biofortification of this medicinal wonder crop through systematic breeding efforts. On the basis of mineral analysis, three genotypes, namely PAU2, PAU4, and PAU16, were found superior in terms of mineral composition in microgreens and mature leaves of celery. Principal component and cluster analyses divide the genotypes into two different clusters on the basis of variability in mineral composition.

Mineral Content Variation in Leaves, Stalks, and Seeds of Celery (Apium graveolens L.) Genotypes.

Celery is an important nutritionally rich crop in the family Apiaceae. It is cultivated worldwide for food as well as for use in pharmaceutics. It is an excellent source of minerals, vitamins, and phytochemicals. Identification of superior genotypes with improved nutritional content is the requirement to develop cultivars for commercial cultivation. For mineral analysis of celery, an experiment was carried out taking 20 diverse genotypes. These genotypes were analysed for macro- and micronutrients which include nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), iron (Fe), zinc (Zn), manganese (Mn), copper (Cu), and sodium (Na). The study revealed high content of K (20.3-26.1 mg/g dry weight (DW)) and Zn (0.09-0.14 mg/g DW) in leaves while the stalks were rich in Ca (41.5-51.3 mg/g DW) and Na (5.2-8.0 mg/g DW). High contents of P (5.2-6.8 mg/g DW), Fe (0.41-0.56 mg/g DW), Cu (0.015-0.026 mg/g DW), and Mn (0.020-0.029 mg/g DW) were observed in seeds. Based on the mineral content, three genotypes, viz., PAU2, PAU4, and PAU7, were found to be superior in terms of mineral composition in leaves, stalks, and seeds. Cluster analysis divided the genotypes into two major groups. These genotypes can be used in crosses as they showed great potential for use in biofortification. This study opens newer avenues for future research, encouraging researchers to enhance the product quality and production efficiency of the leaves, stalks, and seeds valuable for human consumption.

Inheritance and molecular tagging of genes introgressed from Gossypium arboreum to G. hirsutum for leafhopper tolerance.

Cotton cultivation is conquered by transgenic Bt upland cotton hybrids in India. Bt gene does not provide resistance against sucking insect pests. Due to the inherent vulnerability of extant Bt cotton hybrids to sap-sucking insect pests including leafhopper, upland cotton cultivation is seriously threatened by surging populations of these pests. Consistent and extensive screening of upland cotton germplasm over the years has revealed absence of adequate resistance against leafhopper. Here, we report introgression of leafhopper tolerance from a diploid A-genome cotton species, Gossypium arboreum into G. hirsutum. The dominance of leafhopper tolerance was observed over its susceptibility. Genetic analysis revealed that tolerance to leafhopper was inherited in a simple Mendelian fashion and was controlled by two genes, either singly or in combination. Using bulked segregant analysis, two simple-sequence repeat markers, namely NAU 922 and BNL 1705, located on chromosomes A5 and A11 respectively, were tagged with leafhopper tolerance. To the best of our knowledge, this is the first report of molecular tagging of leafhopper tolerance introgressed from G. arboreum into G. hirsutum. A significant negative association was observed between leaf trichome density and leafhopper nymph population.

Molecular mapping of CLCuD resistance introgressed from synthetic cotton polyploid in upland cotton.

Cotton leaf curl disease (CLCuD), caused by a geminivirus complex, is the most serious disease of upland cotton in northwest India and Pakistan. It results in substantial losses in cotton yield and fibre quality. Due to continuous appearance of new viral strains, all the established CLCuD resistant stocks, extant and obsolete cultivars of upland cotton have become susceptible. Therefore, it became crucial to explore the novel sources of CLCuD resistance, as development of CLCuD resistant varieties is the most practical approach to manage this menace. Here, for the first time, we report introgression and mapping of CLCuD resistance from a 'synthetic cotton polyploid' to upland cotton. A backcross population (synthetic polyploid / Gossypium hirsutum Acc. PIL 43/G. hirsutum Acc. PIL 43) was developed for studying inheritance and mapping of CLCuD resistance. Dominance of CLCuD resistance was observed over its susceptibility. Two dominant genes were found to confer resistance to CLCuD. Molecular analysis through genotyping-by-sequencing revealed that chromosomes A01 and D07 harboured one CLCuD resistance gene each.

Genetic analysis of some morphological traits in synthetic x naturally polyploid cotton derivatives.

Cotton has received attention of geneticists since more than a century. Gossypium hirsutum, the predominantly cultivated cotton species worldwide, has a narrow genetic base. It is important to broaden its genetic base through introgression of novel alleles from related species. Here, we report the development and characterization of a backcross population derived from the hybridization of a 'synthetic' (derived by crossing and chromosomal doubling of nonprogenitor Gossypium species) and natural tetraploid upland cotton. 'Synthetic' was observed to be male-sterile and thus, was used as the female parent. A total of 7434 flowers were pollinated to obtain 1868 BC1F1 seeds by direct and reciprocal crosses. Characterization of the experimental plant material was conducted in the field for several morphological traits such as pubescence on the stem, leaf, petiole and bract, presence/absence of petal spot, petal margin colouration and stamen filament colouration. Genetic analysis revealed that petal margin colouration phenotype was governed by a single dominant gene, whereas the petal spot and filament colouration phenotypes manifested segregation distortion. None of the BC1F1 plants was devoid of trichomes thus demonstrating that presence of trichomes is dominant over their absence. Modern upland cotton cultivars are usually devoid of petal spot, petal margin colouration and stamen filament colouration. These floral anthocyanin pigmentation characteristics, if fixed in the cotton germplasm, may serve as diagnostic features for the identification of cultivars during DUS testing as well as in the maintenance breeding programmes.

Identification of genomic regions associated with shoot fly resistance in maize and their syntenic relationships in the sorghum genome.

Shoot fly (Atherigona naqvii) is one of the major insects affecting spring maize in North India and can cause yield loss up to 60 per cent. The genetics of insect resistance is complex as influenced by genotypic background, insect population and climatic conditions. Therefore, quantitative trait loci (QTL) mapping is a highly effective approach for studying genetically complex forms of insect resistance. The objective of the present study was to dissect the genetic basis of resistance and identification of genomic regions associated with shoot fly resistance. A total of 107 F2 population derived from the cross CM143 (resistant) x CM144 (susceptible) was genotyped with 120 SSR markers. Phenotypic data were recorded on replicated F2:3 progenies for various component traits imparting resistance to shoot fly at different time intervals. Resistance to shoot fly was observed to be under polygenic control as evidenced by the identification of 19 putative QTLs governed by overdominance to partial dominance and additive gene actions. The major QTLs conditioning shoot fly resistance viz., qDH9.1 (deadheart) and qEC9.1 (oviposition) explaining 15.03 and 18.89 per cent phenotypic variance, respectively were colocalized on chromosome 9. These QTLs are syntenic to regions of chromosome 10 of sorghum which were also accounted for deadheart and oviposition suggesting that the same gene block may be responsible for shoot fly resistance. The candidate genes such as cysteine protease, subtilisin-chymotrypsin inhibitor, cytochrome P450 involved in synthesis of alleochemicals, receptor kinases, glossy15 and ubiquitin-proteasome degradation pathway were identified within the predicted QTL regions. This is the first reported mapping of QTLs conferring resistance to shoot fly in maize, and the markers identified here will be a valuable resource for developing elite maize cultivars with resistance to shoot fly.

Genomically biased accumulation of seed storage proteins in allopolyploid cotton.

Allopolyploidy is an important process during plant evolution that results in the reunion of two divergent genomes into a common nucleus. Many of the immediate as well as longer-term genomic and epigenetic responses to polyploidy have become appreciated. To investigate the modifications of gene expression at the proteome level caused by allopolyploid formation, we conducted a comparative analysis of cotton seed proteomes from the allopolyploid Gossypium hirsutum (AD genome) and its model A-genome and D-genome diploid progenitors. An unexpectedly high level of divergence among the three proteomes was found, with about one-third of all protein forms being genome specific. Comparative analysis showed that there is a higher degree of proteomic similarity between the allopolyploid and its D-genome donor than its A-genome donor, reflecting a biased accumulation of seed proteins in the allopolyploid. Protein identification and genetic characterization of high-abundance proteins revealed that two classes of seed storage proteins, vicilins and legumins, compose the major component of cotton seed proteomes. Analyses further indicate differential regulation or modification of homoeologous gene products, as well as novel patterns in the polyploid proteome that may result from the interaction between homoeologous gene products. Our findings demonstrate that genomic merger and doubling have consequences that extend beyond the transcriptome into the realm of the proteome and that unequal expression of proteins from diploid parental genomes may occur in allopolyploids.