Integration of conventional and advanced molecular tools to track footprints of heterosis in cotton

Attenuated Total Reflection Fourier Transform Infrared Spectroscopy with Soft Independent Modeling of Class Analogy-Principal Component Analysis for Classifying Cotton Fiber Maturity Phenotypes of Cotton Population Composed of Various Genotypes

Maturity is a major fiber trait that affects the processing and performance of cotton fiber. Rapid and accurate identification of fiber maturity phenotypes and genotypes is of importance to breeders. Previous studies showed that either conventional fiber measurements or attenuated total reflection Fourier transform infrared spectroscopy (ATR FT-IR) analysis discriminated the immature fiber (im) phenotype from the wild type (WT) mature fiber phenotype in a segregating F2 population from a cross between two upland cotton lines differing in fiber maturity. However, both conventional fiber property measurement methods and FT-IR analyses with current algorithms could not detect the subtle differences among the WT fibers composed of two different genotypes, WT homozygosity (WT-homo) and WT heterozygosity (WT-hetero). This research explored the FT-IR method, in combination with soft independent modeling of class analogy of principal component analysis (SIMCA-PCA), for the discrimination of WT fiber phenotypes consisting of two different genotypes (WT-homo and WT-hetero). The new approach enabled the detection of IR spectral intensity differences between WT-homo and WT-hetero fibers. Successful classification originated from a distinctive spectral difference in the low-wavenumber region (<700 cm-1) between WT-hetero fibers and WT-homo fibers. This observation emphasized that ATR FT-IR with a SIMCA-PCA approach would be a sensitive tool for classifying the WT fibers demonstrating minor phenotypic differences. The improved sensitivity of the infrared method may provide a way of dissecting genotype-phenotype interactions of cotton fibers rapidly and efficiently.

Cotton heterosis and hybrid cultivar development

Cotton, the most important economic crop in the world, displays strong hybrid vigor, and has long been a subject for hybrid cultivar breeding. Here, advances in the theoretical and applied research in cotton heterosis along with its hybrid cultivar development by hand-emasculation and pollination (HEP), cytoplasmic (CMS) and genic male sterile lines (GMS) mainly in China during the past few decades are presented in this review. Three types of hybrids produced by HEP, CMS and GMS facilitating hybrid seed production with hand-pollination have been developed and are being planted simultaneously in cotton production. However, most hybrids commercially planted in production are produced by HEP, therefore, F₂ seeds are being extensively planted due to the high cost to produce F₁ seed. F₂ generations of these combinations exceed the check cultivars in yield usually up to 5~15%. GMS genes (ms₂ and ms₅ms₆) used in hybrid seed production and casual mitochondrial genes for G. harknessii CMS have been cloned. Challenges and opportunities in cotton heterosis and future hybrid cultivar development in cotton are discussed.

Transcriptome and Metabolome Analysis of Upland Cotton (Gossypium hirsutum) Seed Pretreatment with MgSO4 in Response to Salinity Stress

Upland cotton (Gossypium hirsutum) is a salt-tolerant crop that can withstand high salinity levels without showing signs of harm to the plant. However, the plant is more prone to salinity stress at the germination stage and a poor germination as well as poor crop stand lead to a weak productivity. It is possible to obtain a comprehensive picture of the cotton seedling germination and establishment against salt stress by examining dynamic changes in the transcriptomic and metabolomic profiles. The reported study employed a pretreatment of cotton seeds by soaking them in 0.2% Magnesium Sulphate (MgSO₄) solution at room temperature for 4, 8, and 12 h. The analysis of variance based on the studied traits emergence rate, above and underground plant parts' fresh weight measured, displayed significant differences of the three treatments compared with the control. A total of 28,801 and 264 differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were discovered to code for biological processes such as response to salt stress, cellular response to salt stress, abscisic acid receptor PYR/PYL, regulation of seed growth and germination, and auxin-activated signaling pathways. A large amount of ethylene-responsive transcription factors (ERF) was identified (1235) as differentially expressed, followed by bHLH (252), WRKY (96), MYB (202), GATA (81), RABA (64), DIVARICATA (28), and MADs-box (26) in treated seedling samples. Functional enrichment analysis revealed the significant roles in the hormones and signal transduction, carbohydrates metabolism, and biosynthesis of amino acids, promoting salt stress tolerance. Our results indicated positive effects of MgSO₄ at 4 h treatment on seedling germination and growth, seemingly by activating certain growth-regulating enzymes (auxins, gibberellins, jasmonates, abscisic acid, and salicylic acid) and metabolites (phenolic acids, flavonoids, and akaloids). Such pretreatment of MgSO₄ on seeds would be beneficial in future cotton management under saline conditions to enhance good crop stand and productivity.

Genetic Factors Underlying Single Fiber Quality in A-Genome Donor Asian Cotton (Gossypium arboreum)

The study of A-genome Asian cotton as a potential fiber donor in Gossypium species may offer an enhanced understanding of complex genetics and novel players related to fiber quality traits. Assessment of individual fibers providing classified fiber quality information to the textile industry is Advanced Fiber Information System (AFIS) in the recent technological era. Keeping the scenario, a diverse collection of 215 Asiatic cotton accessions were evaluated across three agro-ecological zones of China. Genome-Wide Association Studies (GWAS) was performed to detect association signals related to 17 AFIS fiber quality traits grouped into four categories viz: NEPs, fiber length, maturity, and fineness. Significant correlations were found within as well as among different categories of various traits related to fiber quality. Fiber fineness has shown a strong correlation to all other categories, whereas these categories are shown interrelationships via fiber-fineness. A total of 7,429 SNPs were found in association with 17 investigated traits, of which 177 were selected as lead SNPs. In the vicinity of these lead SNPs, 56 differentially expressed genes in various tissues/development stages were identified as candidate genes. This compendium connecting trait-SNP-genes may allow further prioritization of genes in GWAS loci to enable mechanistic studies. These identified quantitative trait nucleotides (QTNs) may prove helpful in fiber quality improvement in Asian cotton through marker-assisted breeding as well as in reviving eroded genetic factors of G. hirsutum via introgression breeding.

Advances in Research on the Mechanism of Heterosis in Plants

Heterosis is a common biological phenomenon in nature. It substantially contributes to the biomass yield and grain yield of plants. Moreover, this phenomenon results in high economic returns in agricultural production. However, the utilization of heterosis far exceeds the level of theoretical research on this phenomenon. In this review, the recent progress in research on heterosis in plants was reviewed from the aspects of classical genetics, parental genetic distance, quantitative trait loci, transcriptomes, proteomes, epigenetics (DNA methylation, histone modification, and small RNA), and hormone regulation. A regulatory network of various heterosis-related genes under the action of different regulatory factors was summarized. This review lays a foundation for the in-depth study of the molecular and physiological aspects of this phenomenon to promote its effects on increasing the yield of agricultural production.

Dissecting Source-Sink Relationship of Subtending Leaf for Yield and Fiber Quality Attributes in Upland Cotton (Gossypium hirsutum L.)

Photosynthesis as a source is a significant contributor to the reproductive sink affecting cotton yield and fiber quality. Moreover, carbon assimilation from subtending leaves adds up a significant proportion to the reproductive sink. Therefore, this study aimed to address the source-sink relationship of boll subtending leaf with fiber quality and yield related traits in upland cotton. A core collection of 355 upland cotton accessions was subjected to subtending leaf removal treatment effects across 2 years. The analysis of variance suggested a significant effect range in the source-sink relationship under subtending leaf removal effects at different growth stages. Further insight into the variation was provided by the correlation analysis and principal component analysis. A significant positive correlation between different traits was observed and the multivariate analysis including hierarchical clustering and principal component analysis (PCA) categorised germplasm accessions into three groups on the basis of four subtending leaf removal treatment effects across 2 years. A set of genotypes with the lowest and highest treatment effects has been identified. Selected accessions and the outcome of the current study may provide a basis for a further study to explore the molecular mechanism of source-sink relationship of boll subtending leaf and utilization of breeding programs focused on cotton improvement.

Genomic insight into the divergence and adaptive potential of a forgotten landrace G. hirsutum L. purpurascens

Wild progenitors are an excellent source for strengthening the genetic basis and accumulation of desirable variation lost because of directional selection and adaptation in modern cultivars. Here, we re-evaluate a landrace of Gossypium hirsutum, formerly known as Gossypium purpurascens. Our study seeks to understand the genomic structure, variation, and breeding potential of this landrace, providing potential insights into the biogeographic history and genomic changes likely associated with domestication. A core set of accessions, including current varieties, obsolete accessions, G. purpurascens, and other geographical landraces, are subjected to genotyping along with multilocation phenotyping. Population fixation statistics suggests a marked differentiation between G. purpurascens and three other groups, emphasizing the divergent genomic behavior of G. purpurascens. Phylogenetic analysis establishes the primitive nature of G. purpurascens, identifying it as a vital source of functional variation, the inclusion of which in the upland cotton (cultivated G. hirsutum) gene pool may broaden the genetic basis of modern cultivars. Genome-wide association results indicate multiple loci associated with domestication regions corresponding to flowering and fiber quality. Moreover, the conserved nature of G. purpurascens can also provide insights into the evolutionary process of G. hirsutum.

GWAS Mediated Elucidation of Heterosis for Metric Traits in Cotton (Gossypium hirsutum L.) Across Multiple Environments

For about a century, plant breeding has widely exploited the heterosis phenomenon-often considered as hybrid vigor-to increase agricultural productivity. The ensuing F₁ hybrids can substantially outperform their progenitors due to heterozygous combinations that mitigate deleterious mutations occurring in each genome. However, only fragmented knowledge is available concerning the underlying genes and processes that foster heterosis. Although cotton is among the highly valued crops, its improvement programs that involve the exploitation of heterosis are still limited in terms of significant accomplishments to make it broadly applicable in different agro-ecological zones. Here, F₁ hybrids were derived from mating a diverse Upland Cotton germplasm with commercially valuable cultivars in the Line × Tester fashion and evaluated across multiple environments for 10 measurable traits. These traits were dissected into five different heterosis types and specific combining ability (SCA). Subsequent genome-wide predictions along-with association analyses uncovered a set of 298 highly significant key single nucleotide polymorphisms (SNPs)/Quantitative Trait Nucleotides (QTNs) and 271 heterotic Quantitative Trait Nucleotides (hQTNs) related to agronomic and fiber quality traits. The integration of a genome wide association study with RNA-sequence analysis yielded 275 candidate genes in the vicinity of key SNPs/QTNs. Fiber micronaire (MIC) and lint percentage (LP) had the maximum number of associated genes, i.e., each with 45 related to QTNs/hQTNs. A total of 54 putative candidate genes were identified in association with HETEROSIS of quoted traits. The novel players in the heterosis mechanism highlighted in this study may prove to be scientifically and biologically important for cotton biologists, and for those breeders engaged in cotton fiber and yield improvement programs.