| Drought resistance is a complex quantitative trait regulated by both genetics and environments.Although cotton is a relatively drought-resistant economic crop,the shortage of water resources has become an important factor restricting the yield and quality of cotton,for that the cotton growing area is gradually moving to the arid north-west region with global warming and the change of crop-planting structure in China.Studying the mechanism of drought resistance,cloning drought-resistant genes and then applying them to cotton breeding is the effective way to solve the shortage of water in the cotton field.At present,the process of discovering and applying drought-resistant genes in cotton is slowly.Although there are some reports on regulatory and functional genes,the progress of researches on drought resistance in cotton still lags behind major food crops,such as maize,rice and wheat.Due to the long growth period,the evaluation index of cotton drought resistance has always been a big problem for researchers.In the current study,a natural population of upland cotton accessions(Gossypium hirsutum Linn.)was used,either to obtain agronomic traits,yield and fiber quality in the field under water-controlled treatment,or to collect a large amount of digital phenotypic indices in greenhouse under drought stress treatment through a phenotyping platform.Combining genome resequencing and transcriptome sequencing data with phenotypic data,genome-wide association study(GWAS)was used to identify important loci and candidate genes related to cotton drought response.The main findings are as follows:1.Comprehensive drought resistance related traits study and association analysis of cotton drought-related traits in fieldIn this study,a natural population consisting of 517 upland cotton accessions were selected for water-limited experiments and association analysis.The water-limited treatment panel was supplied with 50% the water volume of the controls during the whole growth season.A total of 18 traits including agronomic traits,fiber yield indices and fiber quality indices,were investigated at two locations in two years.The phenotypic data were analyzed by BLUP and the drought resistance coefficient of each trait was calculated.The broad-heritability and coefficient of variation of different traits were analyzed.And the correlation networks between each trait were depicted according to the relationship between different traits and water-limited treatment.The results showed that the responses of different varieties to water-limited differed significantly in population.Sixteen traits showed extremely significant differences between the control and the treatment,except for boll weight and fiber uniformity.On the one hand,the water-limited treatment significantly affected fiber quality,as in the decrease of fiber length and the increase of micronaire value.However,50% water-limited treatment increased the cotton yield with seed in fields by 8.46%,and at the same time promoted the establishment of related favorable agronomic traits,which generally shortened the growth period,and then shortened the boll opening stage,as well as reduced the plant height for reasonable dense planting.Combined with the resequencing data of 314 cotton germplasms in this study and resequencing results of 203 germplasms in previous research,a total of 2,564,238 SNPs was obtained for GWAS.Using the drought resistance coefficient(DRC)and the comprehensive index of drought tolerance(CIDT)of different phenotypic traits,33 and 6 QTLs related to drought response were detected respectively,including two novel QTL-hotspot regions.Combined with transcriptome sequencing and q RT-PCR,6 differentially expressed genes(DEGs)were identified in these two QTL-hotspots.This study not only proposed new ideas for water-saving irrigation of cotton field in Xinjiang,but also provided rich genetic evidence and candidate genes for the improvement of cotton drought resistance.2.Phenomics-based GWAS analysis reveals the genetic architecture for drought resistance in cotton at seedling stageThe main methods for drought resistance evaluation in cotton are to establish drought pool,hydroponics experiment or pot drought treatment at seedling stage.And the collection of related indicators is mainly limited to the artificially collected indices such as plant height.In order to high-throughput obtain more indicators for evaluating drought resistance,phenotyping platform was used to conduct dynamic RGB optical imaging of 200 cotton germplasm resources under drought treatment at the seedling stage in the greenhouse.Modeling through manual measurement and non-destructive image extraction,as well as analyzing the correlation between manually collected data and image traits data to verify the reliability of the model,119 image-based digital traits(i-traits)were acquired,including 56 morphological i-traits and 63 texture i-traits.In the study,traditional indices for drought response were verified,such as plant height,plant width and biomass.Moreover,multiple non-artificially acquired i-traits that could accurately reflect the response to drought during the cotton seedling stage were identified,such as morphological i-traits of plant density(PD)and relative frequency(RF),texture i-traits of G component entropy(ET?G),etc.By integrating the performance of various cotton morphological i-traits,the drought resistance of 200 cotton germplasm was divided into three levels that were high resistance,medium resistance and sensitivity.The results showed that phenotyping platform has broken through the bottleneck of manually measured index and provided an excellent technical platform for cotton drought resistance research.The study further combined the genome resequencing data and identified 390 drought-related QTL through GWAS with DRC of different i-traits,including the drought-related genes Gh RD2,Gh NAC4,Gh HAT22 and Gh DREB2 reported in cotton.Two previously unreported tandem repeats Gh DNRs(Gh?A04G0377 and Gh?A04G0378)were identified in a QTL-hotspot using transcriptome data from drought-resistant germplasm ZY168 and drought-sensitive germplasm ZY7.Virus-mediated gene silencing(VIGS)experiments showed that Gh DNRs was a negative regulator of drought resistance in cotton for that the TRV::Gh DNRs cotton plants grew better that control plants.Compared to control plants,the biomass(SA)and plant height of the TRV::Gh DNRs plants were significantly higher,and the defoliation of the cotyledons was delayed,as well as the soluble sugar in leaves was higher in the TRV::Gh DNRs plants under drought treatment.This study used multi-omics such as phenomics,genome resequencing,and transcriptomics,which not only proposed new methods for drought resistance identification of cotton,but also provided basic theoretical and technical support for in-depth analysis of drought resistance mechanism and genetic improvement of drought resistance in cotton. |
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