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Introduction: Defoliation by applying defoliants before machine picking is an important agricultural practice that enhances harvesting efficiency and leads to increased raw cotton purity. However, the fundamental characteristics of leaf abscission and the underlying genetic basis in cotton are not clearly understood. Objectives: In this study, we aimed to (1) reveal the phenotypic variations in cotton leaf abscission, (2) discover the whole-genome differentiation sweeps and genetic loci related to defoliation, (3) identify and verify the functions of key candidate genes associated with defoliation, and (4) explore the relationship between haplotype frequency of loci and environmental adaptability. Methods: Four defoliation-related traits of 383 re-sequenced Gossypium hirsutum accessions were investigated in four environments. The genome-wide association study (GWAS), linkage disequilibrium (LD) interval genotyping and functional identification were conducted. Finally, the haplotype variation related to environmental adaptability and defoliation traits was revealed. Results: Our findings revealed the fundamental phenotypic variations of defoliation traits in cotton. We showed that defoliant significantly increased the defoliation rate without incurring yield and fiber quality penalties. The strong correlations between defoliation traits and growth period traits were observed. A genome-wide association study of defoliation traits identified 174 significant SNPs. Two loci (RDR7 on A02 and RDR13 on A13) that significantly associated with the relative defoliation rate were described, and key candidate genes GhLRR and GhCYCD3;1, encoding a leucine-rich repeat (LRR) family protein and D3-type cell cyclin 1 protein respectively, were functional verified by expression pattern analysis and gene silencing. We found that combining of two favorable haplotypes (HapRDR7 and HapRDR13) improved sensitivity to defoliant. The favorable haplotype frequency generally increased in high latitudes in China, enabling adaptation to the local environment. Conclusion: Our findings lay an important foundation for the potentially broad application of leveraging key genetic loci in breeding machine-pickable cotton.

The most important goal in cotton breeding is to increase the fiber yield which can be increased by improving a key trait, lint percentage (LP). However, narrow genetic background of upland cotton resulting in stagnant yield. In order to effectively dissect the genetic mechanism and enrich the gene loci of LP in cotton, the genetic diversity and population structure and a genome-wide association study (GWAS) was conducted using 204 upland cotton accessions based on 191 pairs of polymorphic microsatellite markers. The results were as follows: (1) The agronomic traits of the materials especially LP varied widely. (2) The SSRs revealed relatively high degree level of genetic diversity at DNA level. (3) Similarity coefficient cluster analysis of SSR markers indicated the influence of male parent on female parents was different after cross, the variation sites of agronomic traits could be further excavate in F1. (4) The GWAS revealed that 3 SSR markers were associated with LP: BNL3649-2, GH0132-2, CIR0246-3. There were two genes, Gh_D02G0125 and Gh_D11G2610, near the three SSR loci. These results provided a theoretical basis for improving fiber yield.

Abstract Background The lateral root is one of the most important organs that constitute the root architecture system in plants. It can directly affect the contact area between plants and soil and plays an important role in plant structural support and nutrient absorption. Optimizing root architecture systems can greatly increase crop yields. This study was designed to identify the molecular markers and candidate genes associated with lateral root development in cotton and to evaluate correlations with yield and disease traits. Result The number of lateral roots for 14-day old seedlings was recorded for 215 Gossypium arboreum accessions. A correlation analysis showed that the number of lateral roots positively correlates with the sympodial branch node and seed index traits, but negatively correlates with lint percentage. A Genome-wide association study (GWAS) identified 18 significant SNPs with 19 candidate genes associated with the lateral root number. Expression analysis identified three genes (FLA12, WRKY29, and RBOHA) associated with lateral root development. Conclusion GWAS analysis identified key SNPs and candidate genes for lateral root number, and genes of FLA12, WRKY29, and RBOHA may play a pivotal role in lateral root development in Asian cotton.

Abstract Background Seedling stage plant biomass is usually used as an auxiliary trait to study plant growth and development or stress adversities. However, few molecular markers and candidate genes of seedling biomass-related traits were found in cotton. Result Here, we collected 215 Gossypium arboreum accessions, and investigated 11 seedling biomass-related traits including the fresh weight, dry weight, water content, and root shoot ratio. A genome-wide association study (GWAS) utilizing 142,5003 high-quality SNPs identified 83 significant associations and 69 putative candidate genes. Furthermore, the transcriptome profile of the candidate genes emphasized higher expression of Ga03G1298, Ga09G2054, Ga10G1342, Ga11G0096, and Ga11G2490 in four representative cotton accessions. The relative expression levels of those five genes were further verified by qRT-PCR. Conclusions The significant SNPs, candidate genes identified in this study are expected to lay a foundation for studying the molecular mechanism for early biomass development and related traits in Asian cotton.

Abstract Upland cotton (Gossypium hirsutum L.) is an important economic crop for renewable textile fibers. However, the simultaneous improvement of yield and fiber quality in cotton is difficult as the linkage drag. Compared with breaking the linkage drag, identification of the favorable pleiotropic loci on the genome level by genome-wide association study (GWAS) provides a new way to improve the yield and fiber quality simultaneously. In our study restriction-site-associated DNA sequencing (RAD-seq) was used to genotype 316 cotton accessions. Eight major traits in three categories including yield, fiber quality and maturation were investigated in nine environments (3 sites × 3 years). 231 SNPs associated with these eight traits (− log10(P) > 5.27) were identified, located in 27 genomic regions respectively by linkage disequilibrium analysis. Further analysis showed that four genomic regions (the region 1, 6, 8 and 23) held favorable pleiotropic loci and 6 candidate genes were identified. Through genotyping, 14 elite accessions carrying the favorable loci on four pleiotropic regions were identified. These favorable pleiotropic loci and elite genotypes identified in this study will be utilized to improve the yield and fiber quality simultaneously in future cotton breeding.

Abstract Background Stem hardness is one of the major influencing factors for plant architecture in upland cotton (Gossypium hirsutum L.). Evaluating hardness phenotypic traits is very important for the selection of elite lines for resistance to lodging in Gossypium hirsutum L. Cotton breeders are interested in using diverse genotypes to enhance fiber quality and high-yield. Few pieces of research for hardness and its relationship with fiber quality and yield were found. This study was designed to find the relationship of stem hardness traits with fiber quality and yield contributing traits of upland cotton. Results Experiments were carried out to measure the bending, acupuncture, and compression properties of the stem from a collection of upland cotton genotypes, comprising 237 accessions. The results showed that the genotypic difference in stem hardness was highly significant among the genotypes, and the stem hardness traits (BL, BU, AL, AU, CL, and CU) have a positive association with fiber quality traits and yield-related traits. Statistical analyses of the results showed that in descriptive statistics result bending (BL, BU) has a maximum coefficient of variance, but fiber length and fiber strength have less coefficient of variance among the genotypes. Principal component analysis (PCA) trimmed quantitative characters into nine principal components. The first nine principal components (PC) with Eigenvalues > 1 explained 86% of the variation among 237 accessions of cotton. Both 2017 and 2018, PCA results indicated that BL, BU, FL, FE, and LI contributed to their variability in PC1, and BU, AU, CU, FD, LP, and FWPB have shown their variability in PC2. Conclusion We describe here the systematic study of the mechanism involved in the regulation of enhancing fiber quality and yield by stem bending strength, acupuncture, and compression properties of G. hirsutum.

Abstract Background Upland cotton (Gossypium hirsutum) accounts for more than 90% of the annual world cotton output because of its high yield potential. However, yield and fiber quality traits often show negative correlations. We constructed four F2 populations of upland cotton, using two normal lines (4133B and SGK9708) with high yield potential but moderate fiber quality and two introgression lines (Suyuan04–3 and J02–247) with superior fiber quality, and used them to investigate the genetic basis underlying complex traits such as yield and fiber quality in upland cotton. We also phenotyped eight agronomic and economic traits and mapped quantitative trait loci (QTLs). Results Extensive phenotype variations and transgressive segregation were found across the segregation populations. We constructed four genetic maps of 585.97 centiMorgan (cM), 752.45 cM, 752.45 cM, and 1 163.66 cM, one for each of the four F2 populations. Fifty QTLs were identified across the four populations (7 for plant height, 27 for fiber quality and 16 for yield). The same QTLs were identified in different populations, including qBW4 and qBW2, which were linked to a common simple sequence repeat (SSR) marker, NAU1255. A QTL cluster containing eight QTLs for six different traits was characterized on linkage group 9 of the 4133B × Suyuan04–3 population. Conclusions These findings will provide insights into the genetic basis of simultaneous improvement of yield and fiber quality in upland cotton breeding.

Growth-regulating factors-interacting factors (GIFs) are a type of transcription co-activators in plants, playing crucial roles in plants’ growth, development, and stress adaptation. Here, a total of 35 GIF genes were identified and clustered into two groups by phylogenetic analysis in four cotton genus. The gene structure and conserved domain analysis proved the conservative characteristics of GIF genes in cotton. The function of GIF genes was evaluated in two cotton accessions, Ji A-1-7 (33xi) and King, which have larger and smaller lateral root numbers, respectively. The results showed that the expression of GhGIF4 in Ji A-1-7 (33xi) was higher than that in King. The enzyme activity and microstructure assay showed a higher POD activity, lower MDA content, and more giant cells of the lateral root emergence part phenotype in Ji A-1-7 (33xi) than in King. A mild waterlogging assay showed the GIF genes were down-regulated in the waterlogged seedling. Further confirmation of the suppression of GhGIF4 in cotton plants further confirmed that GhGIF4 could reduce the lateral root numbers in cotton. This study could provide a basis for future studies of the role of GIF genes in upland cotton.

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.

Abstract Background Gossypium hirsutum L. is grown worldwide and is the largest source of natural fiber crop. We focus on exploring the favorable alleles (FAs) for upland cotton varieties improvement, and further understanding the history of accessions selection and acumination of favorable allele during breeding. Results The genetic basis of phenotypic variation has been studied. But the accumulation of favorable alleles in cotton breeding history in unknown, and potential favorable alleles to enhance key agronomic traits in the future cotton varieties have not yet been identified. Therefore, 419 upland cotton accessions were screened, representing a diversity of phenotypic variations of 7362 G. hirsutum, and 15 major traits were investigated in 6 environments. These accessions were categorized into 3 periods (early, medium, and modern) according to breeding history. All accessions were divided into two major groups using 299 polymorphic microsatellite markers: G1 (high fiber yield and quality, late maturity) and G2 (low fiber yield and quality, early maturity). The proportion of G1 genotype gradually increased from early to modern breeding periods. Furthermore, 21 markers (71 alleles) were significantly associated (−log P > 4) with 15 agronomic traits in multiple environments. Seventeen alleles were identified as FAs; these alleles accumulated more in the modern period than in other periods, consistent with their phenotypic variation trends in breeding history. Our results demonstrate that the favorable alleles accumulated through breeding effects, especially for common favorable alleles. However, the potential elite accessions could be rapidly screened by rare favorable alleles. Conclusion In our study, genetic variation and genome-wide associations for 419 upland cotton accessions were analyzed. Two favorable allele types were identified during three breeding periods, providing important information for yield/quality improvement of upland cotton germplasm.

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.

Abstract Background Heterosis, a multigenic complex trait extrapolated as sum total of many phenotypic features, is widely utilized phenomenon in agricultural crops for about a century. It is mainly focused on establishing vigorous cultivars with the fact that its deployment in crops necessitates the perspective of genomic impressions on prior selection for metric traits. In spite of extensive investigations, the actual mysterious genetic basis of heterosis is yet to unravel. Contemporary crop breeding is aimed at enhanced crop production overcoming former achievements. Leading cotton improvement programs remained handicapped to attain significant accomplishments. Results In mentioned context, a comprehensive project was designed involving a large collection of cotton accessions including 284 lines, 5 testers along with their respective F1 hybrids derived from Line × Tester mating design were evaluated under 10 diverse environments. Heterosis, GCA and SCA were estimated from morphological and fiber quality traits by L × T analysis. For the exploration of elite marker alleles related to heterosis and to provide the material carrying such multiple alleles the mentioned three dependent variables along with trait phenotype values were executed for association study aided by microsatellites in mixed linear model based on population structure and linkage disequilibrium analysis. Highly significant 46 microsatellites were discovered in association with the fiber and yield related traits under study. It was observed that two-thirds of the highly significant associated microsatellites related to fiber quality were distributed on D sub-genome, including some with pleiotropic effect. Newly discovered 32 hQTLs related to fiber quality traits are one of prominent findings from current study. A set of 96 exclusively favorable alleles were discovered and C tester (A971Bt) posited a major contributor of these alleles primarily associated with fiber quality. Conclusions Hence, to uncover hidden facts lying within heterosis phenomenon, discovery of additional hQTLs is required to improve fibre quality. To grab prominent improvement in influenced fiber quality and yield traits, we suggest the A971 Bt cotton cultivar as fundamental element in advance breeding programs as a parent of choice.

Abstract Background Gossypium arboreum is a diploid species cultivated in the Old World. It possesses favorable characters that are valuable for developing superior cotton cultivars. Method A set of 197 Gossypium arboreum accessions were genotyped using 80 genome-wide SSR markers to establish patterns of the genetic diversity and population structure. These accessions were collected from three major G. arboreum growing areas in China. A total of 255 alleles across 80 markers were identified in the genetic diversity analysis. Results Three subgroups were found using the population structure analysis, corresponding to the Yangtze River Valley, North China, and Southwest China zones of G.arboreum growing areas in China. Average genetic distance and Polymorphic information content value of G. arboreum population were 0.34 and 0.47, respectively, indicating high genetic diversity in the G. arboreum germplasm pool. The Phylogenetic analysis results concurred with the subgroups identified by Structure analysis with a few exceptions. Variations among and within three groups were observed to be 13.61% and 86.39%, respectively. Conclusion The information regarding genetic diversity and population structure from this study is useful for genetic and genomic analysis and systematic utilization of economically important traits in G. arboreum.

Abstract Background Cottonseed is one of the most important raw materials for plant protein, oil and alternative biofuel for diesel engines. Understanding the complex genetic basis of cottonseed traits is requisite for achieving efficient genetic improvement of the traits. However, it is not yet clear about their genetic architecture in genomic level. GWAS has been an effective way to explore genetic basis of quantitative traits in human and many crops. This study aims to dissect genetic mechanism seven cottonseed traits by a GWAS for genetic improvement. Results A genome-wide association study (GWAS) based on a full gene model with gene effects as fixed and gene-environment interaction as random, was conducted for protein, oil and 5 fatty acids using 316 accessions and ~ 390 K SNPs. Totally, 124 significant quantitative trait SNPs (QTSs), consisting of 16, 21, 87 for protein, oil and fatty acids (palmitic, linoleic, oleic, myristic, stearic), respectively, were identified and the broad-sense heritability was estimated from 71.62 to 93.43%; no QTS-environment interaction was detected for the protein, the palmitic and the oleic contents; the protein content was predominantly controlled by epistatic effects accounting for 65.18% of the total variation, but the oil content and the fatty acids except the palmitic were mainly determined by gene main effects and no epistasis was detected for the myristic and the stearic. Prediction of superior pure line and hybrid revealed the potential of the QTSs in the improvement of cottonseed traits, and the hybrid could achieve higher or lower genetic values compared with pure lines. Conclusions This study revealed complex genetic architecture of seven cottonseed traits at whole genome-wide by mixed linear model approach; the identified genetic variants and estimated genetic component effects of gene, gene-gene and gene-environment interaction provide cotton geneticist or breeders new knowledge on the genetic mechanism of the traits and the potential molecular breeding design strategy.

Improving yield is a major objective for cotton breeding schemes, and lint yield and its three component traits (boll number, boll weight and lint percentage) are complex traits controlled by multiple genes and various environments. Association mapping was performed to detect markers associated with these four traits using 651 simple sequence repeats (SSRs). A mixed linear model including epistasis and environmental interaction was used to screen the loci associated with these four yield traits by 323 accessions of Gossypium hirsutum L. evaluated in nine different environments. 251 significant loci were detected to be associated with lint yield and its three components, including 69 loci with individual effects and all involved in epistasis interactions. These significant loci explain ∼ 62.05% of the phenotypic variance (ranging from 49.06% ∼ 72.29% for these four traits). It was indicated by high contribution of environmental interaction to the phenotypic variance for lint yield and boll numbers, that genetic effects of SSR loci were susceptible to environment factors. Shared loci were also observed among these four traits, which may be used for simultaneous improvement in cotton breeding for yield traits. Furthermore, consistent and elite loci were screened with -Log10 (P-value) >8.0 based on predicted effects of loci detected in different environments. There was one locus and 6 pairs of epistasis for lint yield, 4 loci and 10 epistasis for boll number, 15 loci and 2 epistasis for boll weight, and 2 loci and 5 epistasis for lint percentage, respectively. These results provided insights into the genetic basis of lint yield and its components and may be useful for marker-assisted breeding to improve cotton production.