Cotton provides natural fiber resources for spinning, and is used by human beings for thousands of years. Traditional breeding methods contributed so much to cotton improvement, but breeders are not able to develop new variety with expectation. Cotton genomics, although complex as a tetraploid, developed so fast recently. The draft genomes for A, D, AD1 and AD2 are published in the recent years, which promoted GWAS analysis of cotton economic traits, with lots of genes identified. The evolution of genomes is described, many structural variations and gene mutations were identified, which will be very helpful for investigating interaction between genes and map-based cloning. We predict more and more genes will be cloned later on, which will be useful for molecular design breeding. Recently the 3D genome of cotton was studied, inter-subgenomic chromatin interactions has revealed the spatial proximity of homoeologous genes, possibly associated with their coordinated expression. The 3D genome study provides a new way in understanding genome structure and transcriptional regulation. The previous publications are surely advanced the knowledge of cotton genomics, but a reference-scale genome should be work out for more exactly designing a variety or molecular assisted breeding.

Gossypium hirsutum L. represents the largest source of textile fibre, and China is one of the largest cotton producing and consuming countries in the world. To investigate the genetic architecture of the agronomic traits of white fiber upland cotton in China, a diverse and nation-wide population containing 503 G. hirsutum accessions was collected for GWAS on 16 agronomic traits. The accessions were planted in four places from 2012 to 2013 for phenotyping. The CottonSNP63K array and a published high-density map based on this array were used for genotyping. A total of 324 SNPs and 160 candidate quantitative trait loci (QTL) regions were identified as significantly associated with the 16 agronomic traits. A network was established for multi-effects in QTLs and inter-associations among traits. Thirty-eight associated regions had pleiotropic effects controlling more than one trait. To understand the genetic basis of brown fibre cotton, an F2 population was constructed to genetically map the dark brown fiber gene in an introgression line with mutant dark brown fiber derived from an interspecific hybridization between Gossypium hirsutum cv. Handan208 and G. barbadense Pima90-53. On the other hand, in order to comprehensively reveal the genetic basis of brown fiber, 100 accessions with light to dark brown fibers were collected, together with 109 re-sequenced white fiber accessions randomly selected from Upland cotton, to construct an association mapping panel. The 100 brown fiber accessions were genotyped by re-sequencing, and phenotyped with 21 of the 109 white fiber accessions in three environments to map quantitative trait loci (QTL) related to fiber color, yield and quality traits by genome-wide association study (GWAS). The brown fibre region, Lc1, was fine-mapped and dissected it into two loci, qBF-A07-1 and qBF-A07-2. The qBF-A07-1 locus mediates the initiation of brown fibre generation, whereas the shade of the brown fibre is affected by the interaction between qBF-A07-1 and qBF-A07-2. Haploid analysis of the signals significantly associated with these two loci showed that most tetraploid modern brown cotton accessions exhibit the introgression signature of G. barbadense. Ten quantitative trait loci (QTLs) for fibre yield and 19 QTLs were identified for fibre quality and found that qBF-A07-2 negatively affects fibre yield and quality through an epistatic interaction with qBF-A07-1. This study sheds light on the genetics of fibre colour and lint-related traits in brown fibre cotton, which will guide the elite cultivars breeding of brown fibre cotton.

Heat and drought represent two of the most common abiotic stresses that plants encounter in modern agricultural production systems and can cause significant economic losses. As climate change continues to increase the frequency and severity of these conditions, the development of stress-resilient cultivars becomes pivotal to sustaining crop yields. To meet these challenges, a better understanding of the genetic control of physiological responses to these environmental conditions is needed. In light of this, we evaluated an upland cotton (Gossypium hirsutum L.) recombinant inbred line (RIL) mapping population under water-limited and well-watered conditions in a hot, arid environment across three years. Ionomic profiling, the rapid quantification of elemental concentrations in a given sample, was used to phenotype seed subsamples from the population. Additionally, soil samples taken from throughout the entire field site were also assayed to better model the soil elemental heterogeneity and account for this variability in subsequent analyses. The elements profiled in seeds exhibited moderate to high heritabilities as well as strong phenotypic and genotypic correlations between elements. Both types of correlations maintained their strength and direction despite the imposed irrigation regimes. Quantitative trait loci (QTL) mapping results from a Bayesian classification method identified multiple genomic regions where QTL for individual elements colocalized, suggesting that genetic control of the ionome is highly interrelated. To more fully exploit this shared genetic architecture, multivariate QTL mapping was implemented among groups of biochemically related elements. This analysis revealed both additional as well as pleiotropic QTL responsible for the coordinated control of phenotypic variation for elemental accumulation in seeds. To further leverage these data to gain insight into the physiological status of the plants, machine learning algorithms that utilized only ionomic data were used to predict the irrigation under which RIL lines were grown. The best performing method, which was support vector machines, produced a prediction accuracy of 97.7% providing empirical evidence that ionome can capture the physiological status of the plant. Taken together, these results demonstrate the extent to which the seed ionome is genetically interrelated and predictive of plant physiological response to adverse environmental conditions.

Short-season cotton varieties were cultivated to increase cropping index, and they also were introduced to the short frost-free areas for expanding the cotton planting area in China. The report described 1) the selection basis of early maturity traits of cotton varieties, 2) genetic characteristics of early maturity traits in cotton varieties, 3) early maturity related gene cloning and 4) early maturity cotton breeding. In terms of selection of early maturity traits, seedling period, boll period, node of first fruiting branch, plant height and yield percentage before frost were mainly controlled by genetic inheritance, which could be used as an indicator of early maturity. In the aspects of early maturity genetic traits, the heritability of flowering stage was controlled by both additive and dominant genes. The genetic analysis of the Upland cotton showed that there were significant additive effects at flowering period and boll opening period. Node of first fruiting branch, plant height and mature period showed additive and dominant effects significantly, but dominated by the dominant effect. The genetic map was constructed using early maturity cotton varieties, which mainly focused on seedling period, bud period, flowering period, flower and boll period, growth period, yield percentage before frost, the first fruit branch node, node of first fruiting branch, boll opening period. At the same time, cotton flowering related genes such as FPF1 (FLOWERING PROMOTING FACTOR 1), SOC1 (SUPPRESSOR OF OVEREXPRESSION OF CO 1), CO (CONSTANS), LFY (LEAFY) and AP1 (APETALA1) were cloned and their function needs to be further verified. Hybridization breeding was mainly applied in early maturity cotton breeding. The parents should be complementary, one of the parents is an extremely early mature type or the two parents are more mature materials which often appear of the super-separation in the maturity. The selection of parents should have high general combining abilities. The application of short-season cotton was summarized in China's Yellow River cotton area, the Yangtze River cotton area and the northwest inland cotton area, and the main problems and countermeasures were overviewed briefly,, which provided a reference for short-season cotton breeding in research and utilization.