Genome-Wide Association Analysis of Salt-Tolerant Traits in Terrestrial Cotton at Seedling Stage

Integrative physiology and transcriptome sequencing reveal differences between G. hirsutum and G. barbadense in response to salt stress and the identification of key salt tolerance genes

BACKGROUND

Soil salinity is one of the major abiotic stresses that threatens crop growth. Cotton has some degree of salt tolerance, known as the "pioneer crop" of saline-alkali land. Cultivation of cotton is of great significance to the utilization of saline-alkali land and the development of cotton industry. Gossypium hirsutum and G. barbadense, as two major cotton species, are widely cultivated worldwide. However, until recently, the regulatory mechanisms and specific differences of their responses to salt stress have rarely been reported.

RESULTS

In this study, we comprehensively compared the differences in the responses of G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 to salt stress. The results showed that Hai7124 exhibited better growth than did TM-1 under salt stress, with greater PRO content and antioxidant capability, whereas TM-1 only presented greater K+ content. Transcriptome analysis revealed significant molecular differences between the two cotton species in response to salt stress. The key pathways of TM-1 induced by salt are mainly related to growth and development, such as porphyrin metabolism, DNA replication, ribosome and photosynthesis. Conversely, the key pathways of Hai7124, such as plant hormone signal transduction, MAPK signaling pathway-plant, and phenylpropanoid biosynthesis, are mainly related to plant defense. Further comparative analyses of differentially expressed genes (DEGs) revealed that antioxidant metabolism, abscisic acid (ABA) and jasmonic acid (JA) signalling pathways were more strongly activated in Hai7124, whereas TM-1 was more active in K+ transporter-related genes and ethylene (ETH) signalling pathway. These differences underscore the various molecular strategies adopted by the two cotton species to navigate through salt stress, and Hai7124 responded more strongly to salt stress, which explains the potential reasons for the greater salt tolerance of Hai7124. Finally, we identified 217 potential salt tolerance-related genes, 167 of which overlapped with the confidence intervals of significant SNPs identified in previous genome-wide association studies (GWASs), indicating the high reliability of these genes.

CONCLUSIONS

These findings provide new insights into the differences in the regulatory mechanisms of salt tolerance between G. hirsutum and G. barbadense, and identify key candidate genes for salt tolerance molecular breeding in cotton.

Impact of ZnO NPs on photosynthesis in rice leaves plants grown in saline-sodic soil

Saline-sodic stress restricts the absorption of zinc by rice, consequently impacting the photosynthesis process of rice plants. In this experiment, Landrace 9 was selected as the test material and the potting method was employed to investigate the influence of ZnO nanoparticles (ZnO NPs) on zinc absorption and chlorophyll fluorescence in rice grown in saline-sodic land. The research findings demonstrate that the application of ZnO NPs proves to be more advantageous for the growth of rice in saline-sodic soil. Notably, the application of ZnO NPs significantly decreases the levels of Na+ and MDA in rice leaves in saline-sodic soil, while increasing the levels of K+ and Zn2+. Additionally, ZnO NPs enhances the content of chloroplast pigments, specific energy flux, quantum yield, and the performance of active PSII reaction center (PIABS) in rice leaves under saline-sodic stress. Furthermore, the relative variable fluorescence (WK and VJ) and quantum energy dissipation rate (φDo) of rice are also reduced. Therefore, the addition of ZnO NPs enhances the transfer of electrons and energy within the rice photosystem when subjected to saline-sodic stress. This promotes photosynthesis in rice plants growing in saline-sodic land, increasing their resistance to saline-sodic stress and ultimately facilitating their growth and development.

Identification of novel candidate loci and genes for seed vigor-related traits in upland cotton (Gossypium hirsutum L.) via GWAS

Seed vigor (SV) is a crucial trait determining the quality of crop seeds. Currently, over 80% of China's cotton-planting area is in Xinjiang Province, where a fully mechanized planting model is adopted, accounting for more than 90% of the total fiber production. Therefore, identifying SV-related loci and genes is crucial for improving cotton yield in Xinjiang. In this study, three seed vigor-related traits, including germination potential, germination rate, and germination index, were investigated across three environments in a panel of 355 diverse accessions based on 2,261,854 high-quality single-nucleotide polymorphisms (SNPs). A total of 26 significant SNPs were detected and divided into six quantitative trait locus regions, including 121 predicted candidate genes. By combining gene expression, gene annotation, and haplotype analysis, two novel candidate genes (Ghir_A09G002730 and Ghir_D03G009280) within qGR-A09-1 and qGI/GP/GR-D03-3 were associated with vigor-related traits, and Ghir_A09G002730 was found to be involved in artificial selection during cotton breeding by population genetic analysis. Thus, understanding the genetic mechanisms underlying seed vigor-related traits in cotton could help increase the efficiency of direct seeding by molecular marker-assisted selection breeding.

Genome-wide association study of drought tolerance traits in sugar beet germplasms at the seedling stage

Introduction: Sugar beets are an important crop for global sugar production. Intense drought and the increasing lack of water resources pose a great threat to sugar beet cultivation. It is a priority to investigate favourable germplasms and functional genes to improve the breeding of drought tolerant plants. Methods: Thus, in this study, 328 sugar beet germplasms were used in a genome-wide association study (GWAS) to identify single nucleotide polymorphism (SNP) markers and candidate genes associated with drought tolerance. Results: The results showed that under drought stress (9% PEG-6000), there were 11 significantly associated loci on chromosomes 2, 3, 5, 7, and 9 from the 108946 SNPs filtered using a mixed linear model (MLM). Genome-wide association analysis combined with qRT-PCR identified 13 genes that were significantly differentially expressed in drought-tolerant extreme materials. Discussion: These candidate genes mainly exhibited functions such as regulating sugar metabolism, maintaining internal environmental stability and participating in photosystem repair. This study provides valuable information for exploring the molecular mechanisms of drought tolerance and improvement in sugar beet.

Integration of GWAS and RNA-Seq Analysis to Identify SNPs and Candidate Genes Associated with Alkali Stress Tolerance at the Germination Stage in Mung Bean

Soil salt-alkalization seriously impacts crop growth and productivity worldwide. Breeding and applying tolerant varieties is the most economical and effective way to address soil alkalization. However, genetic resources for breeders to improve alkali tolerance are limited in mung bean. Here, a genome-wide association study (GWAS) was performed to detect alkali-tolerant genetic loci and candidate genes in 277 mung bean accessions during germination. Using the relative values of two germination traits, 19 QTLs containing 32 SNPs significantly associated with alkali tolerance on nine chromosomes were identified, and they explained 3.6 to 14.6% of the phenotypic variance. Moreover, 691 candidate genes were mined within the LD intervals containing significant trait-associated SNPs. Transcriptome sequencing of alkali-tolerant accession 132-346 under alkali and control conditions after 24 h of treatment was conducted, and 2565 DEGs were identified. An integrated analysis of the GWAS and DEGs revealed six hub genes involved in alkali tolerance responses. Moreover, the expression of hub genes was further validated by qRT-PCR. These findings improve our understanding of the molecular mechanism of alkali stress tolerance and provide potential resources (SNPs and genes) for the genetic improvement of alkali tolerance in mung bean.

Genomic Dynamics and Functional Insights under Salt Stress in Gossypium hirsutum L

The changing climate is intensifying salt stress globally. Salt stress is a menace to cotton crop quality and yield. The seedling, germination, and emergence phases are more prone to the effects of salt stress than other stages. Higher levels of salt can lead to delayed flowering, a reduced number of fruiting positions, shedding of fruits, decreased boll weight, and yellowing of fiber, all of which have an adverse effect on the yield and quality of the seed cotton. However, sensitivity toward salt stress is dependent on the salt type, cotton growth phase, and genotype. As the threat of salt stress continues to grow, it is crucial to gain a comprehensive understanding of the mechanisms underlying salt tolerance in plants and to identify potential avenues for enhancing the salt tolerance of cotton. The emergence of marker-assisted selection, in conjunction with next-generation sequencing technologies, has streamlined cotton breeding efforts. This review begins by providing an overview of the causes of salt stress in cotton, as well as the underlying theory of salt tolerance. Subsequently, it summarizes the breeding methods that utilize marker-assisted selection, genomic selection, and techniques for identifying elite salt-tolerant markers in wild species or mutated materials. Finally, novel cotton breeding possibilities based on the approaches stated above are presented and debated.

Transcriptome Revealed GhPP2C43-A Negatively Regulates Salinity Tolerance in an Introgression Line from a Semi-wild Upland Cotton

Salt damage is one of the major threats to sustainable cotton production owing to the limited arable land in China mainly occupied by the production of staple food crops. Salt-stress tolerant cotton varieties are lacking in production and, the mechanisms underpinning salt-stress tolerance in cotton remain enigmatic. Here, DM37, an intraspecific introgression line from G. hirsutum race yucatanense acc TX-1046 into the G. hirsutum acc TM-1 background, was found to be highly tolerant to salt stress. Its seed germination rate and germination potential were significantly higher than the recipient TM-1 under salt stress. Physiological analysis showed DM37 had higher proline content and Peroxidase activity, as well as lower Na+/K+ ratios at the seedling stage, consistent with higher seedling survival rate after durable salt stress. Furthermore, comparative transcriptome analysis revealed that responsive patterns to salt stress in DM37 were different from TM-1. Weighted Correlation Network Analysis (WGCNA) demonstrated that co-expression modules associated with salt stress in DM37 also differed from TM-1. Out of them, GhPP2C43-A, a phosphatase gene, exhibited negative regulation of salt-stress tolerance verified by VIGS and transgenic Arabidopsis. Gene expression showed GhPP2C43-A in TM-1 was induced by durable salt stress but not in DM37 probably attributing to the variation of cis-element in its promoter, thereby being conferred different salt-stress tolerance. Our result would provide new genes/germplasms from semi-wild cotton in salt-stress tolerant cotton breeding. This study would give us new insights into the mechanisms underpinning the salt-stress tolerance in cotton.

Identification of Salt Tolerance Related Candidate Genes in 'Sea Rice 86' at the Seedling and Reproductive Stages Using QTL-Seq and BSA-Seq

Salt stress seriously affects plant growth and development and reduces the yield of rice. Therefore, the development of salt-tolerant high-yielding rice cultivars through quantitative trait locus (QTL) identification and bulked segregant analysis (BSA) is the main focus of molecular breeding projects. In this study, sea rice (SR86) showed greater salt tolerance than conventional rice. Under salt stress, the cell membrane and chlorophyll were more stable and the antioxidant enzyme activity was higher in SR86 than in conventional rice. Thirty extremely salt-tolerant plants and thirty extremely salt-sensitive plants were selected from the F2 progenies of SR86 × Nipponbare (Nip) and SR86 × 9311 crosses during the whole vegetative and reproductive growth period and mixed bulks were generated. Eleven salt tolerance related candidate genes were located using QTL-seq together with BSA. Real time quantitative PCR (RT-qPCR) analysis showed that LOC_Os04g03320.1 and BGIOSGA019540 were expressed at higher levels in the SR86 plants than in Nip and 9311 plants, suggesting that these genes are critical for the salt tolerance of SR86. The QTLs identified using this method could be effectively utilized in future salt tolerance breeding programs, providing important theoretical significance and application value for rice salt tolerance breeding.

Genome-Wide Association Study (GWAS) and genome prediction of seedling salt tolerance in bread wheat (Triticum aestivum L.)

BACKGROUND

Salinity tolerance in wheat is imperative for improving crop genetic capacity in response to the expanding phenomenon of soil salinization. However, little is known about the genetic foundation underlying salinity tolerance at the seedling growth stage of wheat. Herein, a GWAS analysis was carried out by the random-SNP-effect mixed linear model (mrMLM) multi-locus model to uncover candidate genes responsible for salt tolerance at the seedling stage in 298 Iranian bread wheat accessions, including 208 landraces and 90 cultivars.

RESULTS

A total of 29 functional marker-trait associations (MTAs) were detected under salinity, 100 mM NaCl (sodium chloride). Of these, seven single nucleotide polymorphisms (SNPs) including rs54146, rs257, rs37983, rs18682, rs55629, rs15183, and rs63185 with R² ≥ 10% were found to be linked with relative water content, root fresh weight, root dry weight, root volume, shoot high, proline, and shoot potassium (K⁺), respectively. Further, a total of 27 candidate genes were functionally annotated to be involved in response to the saline environment. Most of these genes have key roles in photosynthesis, response to abscisic acid, cell redox homeostasis, sucrose and carbohydrate metabolism, ubiquitination, transmembrane transport, chromatin silencing, and some genes harbored unknown functions that all together may respond to salinity as a complex network. For genomic prediction (GP), the genomic best linear unbiased prediction (GBLUP) model reflected genetic effects better than both bayesian ridge regression (BRR) and ridge regression-best linear unbiased prediction (RRBLUP), suggesting GBLUP as a favorable tool for wheat genomic selection.

CONCLUSION

The SNPs and candidate genes identified in the current work can be used potentially for developing salt-tolerant varieties at the seedling growth stage by marker-assisted selection.

Status and prospects of genome-wide association studies in cotton

Over the last two decades, the use of high-density SNP arrays and DNA sequencing have allowed scientists to uncover the majority of the genotypic space for various crops, including cotton. Genome-wide association study (GWAS) links the dots between a phenotype and its underlying genetics across the genomes of populations. It was first developed and applied in the field of human disease genetics. Many areas of crop research have incorporated GWAS in plants and considerable literature has been published in the recent decade. Here we will provide a comprehensive review of GWAS studies in cotton crop, which includes case studies on biotic resistance, abiotic tolerance, fiber yield and quality traits, current status, prospects, bottlenecks of GWAS and finally, thought-provoking question. This review will serve as a catalog of GWAS in cotton and suggest new frontiers of the cotton crop to be studied with this important tool.

Spanish Melon Landraces: Revealing Useful Diversity by Genomic, Morphological, and Metabolomic Analysis

Spain is a secondary centre of the diversification of the melon (Cucumis melo L.), with high diversity represented in highly appreciated landraces belonging to the Flexuosus and Ibericus groups. A collection of 47 accessions of Flexuosus, Chate, Piel de Sapo, Tendral, Amarillo, Blanco, and Rochet was analysed using a genotyping-by-sequencing (GBS) approach. A total of 66,971 quality SNPs were identified. Genetic analysis differentiated Ibericus accessions and exotic materials (Ameri, Momordica, Kachri, and Agrestis), while Flexuous accessions shared ancestry between them. Within the Ibericus group, no clear genomic distinction could be identified for the different landraces evaluated, with accessions of different landraces showing high genetic similarity. The morphological characterization confirmed that the external colour and fruit shape had been used as recognition patterns for Spanish melon landraces, but variability within a landrace exists. Differences were found in the sugars and acid and volatile profiles of the materials. Flexuosus and Chate melons at the immature commercial stage accumulated malic acid and low levels of hexoses, while Ibericus melons accumulated high contents of sucrose and citric acid. Specific trends could be identified in the Ibericus landraces. Tendral accumulated low levels of sugars and citric acid and high of malic acid, maintaining higher firmness, Rochet reached higher levels of sugars, and Amarillo tended to lower malic acid contents. Interestingly, high variability was found within landraces for the acidic profile, offering possibilities to alter taste tinges. The main volatile organic compounds (VOCs) in Flexuosus and Chate were aldehydes and alcohols, with clear differences between both groups. In the Ibericus landraces, general trends for VOC accumulation could be identified, but, again, a high level of variation exists. This situation highlights the necessity to develop depuration programs to promote on-farm in situ conservation and, at the same time, offers opportunities to establish new breeding program targets and to take advantage of these sources of variation.