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

Plants ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 97
Author(s):  
Juyun Zheng ◽  
Zeliang Zhang ◽  
Zhaolong Gong ◽  
Yajun Liang ◽  
Zhiwei Sang ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Gossypium Hirsutum ◽  
Germination Rate ◽  
Snp Markers ◽  
Tolerance Index ◽  
Salt Tolerant ◽  
Germination Potential ◽  
Genome Wide ◽  
Drop Rate ◽  
Radicle Length

Soil salinization is the main abiotic stress factor affecting agricultural production worldwide, and salt stress has a significant impact on plant growth and development. Cotton is one of the most salt-tolerant crops. Therefore, the selection and utilization of salt-tolerant germplasm resources and the excavation of salt resistance genes play important roles in improving cotton production in saline–alkali soils. In this study, we analysed the population structure and genetic diversity of a total 149 cotton plant materials including 137 elite Gossypium hirsutum cultivar accessions collected from China and 12 elite Gossypium hirsutum cultivar accessions collected from around the world. Illumina Cotton SNP 70 K was used to obtain genome-wide single-nucleotide polymorphism (SNP) data for 149 elite Gossypium hirsutum cultivar accessions, and 18,430 highly consistent SNP loci were obtained by filtering. It was assessed by using PCA principal component analysis so that the 149 elite Gossypium hirsutum cultivar accessions could be divided into two subgroups, including subgroup 1 with 78 materials and subgroup 2 with 71 materials. Using the obtained SNP and other marker genotype test results, under salt stress, the salt tolerance traits 3d Germination potential, 3d Radicle length drop rate, 7d Germination rate, 7d Radicle length drop rate, 7d Germination weight, 3d Radicle length, 7d Radicle length, Relative Germination potential, Relative Germination rate, 7d Radicle weight drop rate, Salt tolerance index 3d Germination potential index, 3d Radicle length index, 7d Radicle length index, 7d Radicle weight index and 7d Germination rate index were evaluated by GWAS (genome-wide association analysis). A total of 27 SNP markers closely related to the salt tolerance traits and 15 SNP markers closely related to the salt tolerance index were detected. At the SNP locus associated with phenotyping, Gh_D01G0943, Gh_D01G0945, Gh_A01G0906, Gh_A01G0908, Gh_D08G1308 and Gh_D08G1309 related to plant salt tolerance were detected, and they were found to be involved in intracellular transport, sucrose synthesis, osmotic pressure balance, transmembrane transport, N-glycosylation, auxin response and cell amplification. This study provides a theoretical basis for the selection and breeding of salt-tolerant upland cotton varieties.

scholarly journals Genome-wide association analysis of cotton salt stress response-related sites

2021 ◽  
Author(s):  
Zeliang Zhang ◽  
Juyun Zheng ◽  
Zhaolong Gong ◽  
Yajun Liang ◽  
Zhiwei Sang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Association Analysis ◽  
Upland Cotton ◽  
Snp Markers ◽  
Tolerance Index ◽  
Salt Tolerant ◽  
Salt Stress Response ◽  
Genome Wide ◽  
Salt Tolerance Index

Soil salinization is the main abiotic stress factor affecting agricultural production worldwide, and salt stress has a significant impact on plant growth and development. Cotton is one of the most salt-tolerant crops. Its salt tolerance varies greatly depending on the variety, growth stage, organs, and soil salt types. Therefore, the selection and utilization of excellent salt-tolerant germplasm resources and the excavation of excellent salt-tolerant salt and salt resistance genes play important roles in improving cotton production in saline-alkali soils. In this study, we analysed the population structure and genetic diversity of 144 elite Gossypium hirsutum cultivar accessions collected from around the world, and especially from China. Illumina Cotton SNP 70K was used to obtain genome-wide single-nucleotide polymorphism (SNP) data for 149 experimental materials, and 18,432 highly consistent SNP loci were obtained by filtering. PCA (principal component analysis)indicated that 149 upland cotton materials could be divided into 2 subgroups, including subgroup 1 with 78 materials and subgroup 2 with 71 materials. Using the obtained SNP and other marker genotype test results, under salt stress, the salt tolerance traits 3d_Germination_potential, 3d_Bud_length_drop_rate, 7d_Germination_rate, 7d_Bud_length_drop_rate, 7d_Germination_weight, 3d_Bud_length, 7d_Bud_length, relative_germination_potential, Relative_germination_rate, 7d_Bud_weight_drop_rate, Salt tolerance index 3d_Germination_potential_index, 3d_Bud_length_index, 7d_Bud_length_index, 7d_Bud_weight_index, and 7d_Germination_rate_index were evaluated by genome association analysis. A total of 27 SNP markers closely related to salt tolerance traits and 15 SNP markers closely related to salt tolerance index were detected. At the SNP locus associated with the traits of the bud length decline rate at 7 days, alleles Gh_A01G0034 and Gh_D01G0028 related to plant salt tolerance were detected, and they are related to intracellular transport, membrane microtubule formation and actin network. This study provides a theoretical basis for the selection and breeding of salt-tolerant upland cotton varieties.

Responses of seed germination, seedling growth under salinity stresses and variability for phenotypic traits in Tossa Jute (Corchorus olitorius L.)

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Md. Mia Mukul ◽  
Sheikh Shorif Uddin Ahmed ◽  
Nargis Akter ◽  
Md. Golam Mostofa ◽  
Md. Sohanur Rahman ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Seed Germination ◽  
Germination Rate ◽  
Phenotypic Traits ◽  
Tolerance Index ◽  
Corchorus Olitorius ◽  
Salt Tolerant ◽  
Fiber Yield ◽  
Good For ◽  
Salt Tolerance Index

Salinity is a serious abiotic stress to Jute and other crop cultivation at saline regions in the world. No salt tolerant Tossa Jute (Corchorus olitorius L.) variety was developed in Bangladesh. Hence, six Tossa Jute accessions were investigated at germination stage against six concentration levels (0.00 or d.H2O, 8.0, 10.0, 12.0, 14.0 and 16.0 dS m-1) of salt (NaCl) using RCB design at Bangladesh Jute Research Institute (BJRI) during March-July, 2020. Jute seeds collected from Gene Bank of BJRI were allowed to germinate under laboratory condition. Seed germination rate was adversely affected as well as delay in germination was prolonged with increasing the salt concentration. In control, seeds were germinated up to 14.0 dS m-1 salt solution. Among six genotypes, Acc. 1141 and Acc. 3801 showed the highest germination rate (86.67 %); Acc. 3801 gave maximum root length (17.0 mm), dry biomass (6.37 mg); and Acc. 1089 showed higher shoot length (10.0 mm), fresh weight (43.93 mg) and salt tolerance index (60.69 %) under 14.0 dS m-1 level. Higher relative salt harm rate (7.14 %) was observed in both Acc. 1141 and Acc. 3801 under 14.0 dS m-1 salinity indicating highly tolerance to salinity. Acc. 3801 and Acc. 1141 were found good for germination under salt stresses; Acc. 3801, Acc. 1089 for fiber yield and salt tolerance; Acc. 3801 and Acc. 1407 for higher fiber yield. Acc. 3801 was found good for salt tolerance and fiber yield content. The genotypes with good desirable characters would be used as breeding materials to develop high yielding salt tolerant Tossa Jute variety.

scholarly journals Evaluation of Salt Tolerance at Germination Stage in Cowpea [Vigna unguiculata (L.) Walp]

HortScience ◽  
2017 ◽  
Vol 52 (9) ◽  
pp. 1168-1176 ◽  
Author(s):  
Waltram Second Ravelombola ◽  
Ainong Shi ◽  
Yuejin Weng ◽  
John Clark ◽  
Dennis Motes ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Seed Germination ◽  
Salinity Stress ◽  
Germination Rate ◽  
Correlation Coefficients ◽  
Human Consumption ◽  
Tolerance Index ◽  
Salt Tolerant ◽  
Salt Tolerance Index ◽  
Germination Stage

Cowpea is a leguminous and versatile crop which provides nutritional food for human consumption. However, salinity unfavorably reduces cowpea seed germination, thus significantly decreasing cowpea production. Little has been done for evaluating and developing salt-tolerant cowpea genotypes at germination stage. The objectives of this research were to evaluate the response of cowpea genotypes to salinity stress through seed germination rate and to select salt-tolerant cowpea genotypes. The seed germination rates under nonsalt condition and salinity stress (150 mm NaCl) were evaluated in 151 cowpea genotypes. Four parameters, absolute decrease (AD), the inhibition index (II), the relative salt tolerance (RST), and the salt tolerance index (STI) were used to measure salt tolerance in cowpea. The results showed that there were significant differences among the 151 cowpea genotypes for all parameters (P values <0.0001). The AD in germination rate was 5.8% to 94.2%; the II varied from 7.7% to 100%; the RST ranged from 0 to 0.92; and STI varied from 0 to 0.92. A high broad sense heritability (H2) was observed for all four parameters. High correlation coefficients (r) were estimated among the four parameters. PI582422, 09–529, PI293584, and PI582570 were highly salt tolerant at germination stage. In addition, genotypes from the Caribbean and Southern Asia exhibited better tolerance to salinity, whereas those from Europe and North America were the most salt-susceptible.

scholarly journals Whole genome sequence analysis of rice genotypes with contrasting response to salinity stress

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Prasanta K. Subudhi ◽  
Rama Shankar ◽  
Mukesh Jain
Keyword(s):  
Salt Tolerance ◽  
Dna Polymorphisms ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Salt Tolerant ◽  
Tolerance Mechanisms ◽  
Rice Varieties ◽  
Genome Wide ◽  
Rice Genotypes ◽  
Genome Level

AbstractSalinity is a major abiotic constraint for rice farming. Abundant natural variability exists in rice germplasm for salt tolerance traits. Since few studies focused on the genome level variation in rice genotypes with contrasting response to salt stress, genomic resequencing in diverse genetic materials is needed to elucidate the molecular basis of salt tolerance mechanisms. The whole genome sequences of two salt tolerant (Pokkali and Nona Bokra) and three salt sensitive (Bengal, Cocodrie, and IR64) rice genotypes were analyzed. A total of 413 million reads were generated with a mean genome coverage of 93% and mean sequencing depth of 18X. Analysis of the DNA polymorphisms revealed that 2347 nonsynonymous SNPs and 51 frameshift mutations could differentiate the salt tolerant from the salt sensitive genotypes. The integration of genome-wide polymorphism information with the QTL mapping and expression profiling data led to identification of 396 differentially expressed genes with large effect variants in the coding regions. These genes were involved in multiple salt tolerance mechanisms, such as ion transport, oxidative stress tolerance, signal transduction, and transcriptional regulation. The genome-wide DNA polymorphisms and the promising candidate genes identified in this study represent a valuable resource for molecular breeding of salt tolerant rice varieties.

Comparative studies on salt tolerance of seedlings for one cultivar of puccinellia (Puccinellia ciliata) and two cultivars of tall wheatgrass (Thinopyrum ponticum)

2005 ◽  
Vol 45 (4) ◽  
pp. 391 ◽  
Author(s):  
B. Zhang ◽  
B. C. Jacobs ◽  
M. O'Donnell ◽  
J. Guo
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Seed Germination ◽  
Germination Rate ◽  
Seedling Emergence ◽  
Salt Tolerant ◽  
Mineral Contents ◽  
Shoot Height ◽  
Thinopyrum Ponticum ◽  
Tall Wheatgrass

Salt tolerances of 3 cultivars, Menemen puccinellia (Puccinellia ciliata Bor), Tyrrell and Dundas [tall wheatgrass, Thinopyrum ponticum (Podp.) Z. W. Liu and R. R. C. Wang], were compared with respect to their seed germination, adaptive responses to salt and waterlogging, seedling emergence, plant growth, shoot osmolality and mineral contents in a series of salt-stress experiments. An inverse normal distribution provided good fits for the time to seed germination. Under NaCl stress, 50% of the control (distilled water) seed germination rates of Menemen, Tyrrell and Dundas were achieved in 178.8, 300.9 and 296.8 mmol/L NaCl, respectively. Fifty percent of the control seedling emergence rates of these 3 cultivars were in 92.7, 107.2 and 113.5 mmol/L NaCl, respectively. The seed germination rates of these 3 cultivars under both salt and waterlogging stress were far lower than those germinated only under salt stress at the same salt level. Seed pretreatment by soaking seed in NaCl solutions greatly increased the seed germination rate under salt stress for Menemen and under both salt stress and waterlogging for Dundas. Tyrrell and Dundas were very similar in their tolerance to salt stress, and were significantly (P<0.05) more salt tolerant than Menemen in terms of seed germination and seedling emergence rate. Both shoot height and dry matter of these 3 cultivars were not statistically different among all salt stress levels during the seedling elongation period, indicating that the established plants of these 3 cultivars were very salt tolerant. The salt tolerance mechanisms of these 3 cultivars are possibly related to their abilities to maintain high osmolality in shoots by regulating high sodium and potassium contents, and reducing calcium deficiency under salt stress.

scholarly journals Characterization of Maize Hybrids (Zea mays L.) for Detecting Salt Tolerance Based on Morpho-Physiological Characteristics, Ion Accumulation and Genetic Variability at Early Vegetative Stage

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2549
Author(s):  
Md Al Samsul Huqe ◽  
Md Sabibul Haque ◽  
Ashaduzzaman Sagar ◽  
Md Nesar Uddin ◽  
Md Alamgir Hossain ◽  
...  
Keyword(s):  
Multivariate Analysis ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Dry Weight ◽  
Ion Accumulation ◽  
Growth And Yield ◽  
Tolerance Index ◽  
Salt Tolerant ◽  
Maize Cultivars ◽  
Root Shoot Ratio

Increasing soil salinity due to global warming severely restricts crop growth and yield. To select and recommend salt-tolerant cultivars, extensive genotypic screening and examination of plants’ morpho-physiological responses to salt stress are required. In this study, 18 prescreened maize hybrid cultivars were examined at the early growth stage under a hydroponic system using multivariate analysis to demonstrate the genotypic and phenotypic variations of the selected cultivars under salt stress. The seedlings of all maize cultivars were evaluated with two salt levels: control (without NaCl) and salt stress (12 dS m−1 simulated with NaCl) for 28 d. A total of 18 morpho-physiological and ion accumulation traits were dissected using multivariate analysis, and salt tolerance index (STI) values of the examined traits were evaluated for grouping of cultivars into salt-tolerant and -sensitive groups. Salt stress significantly declined all measured traits except root–shoot ratio (RSR), while the cultivars responded differently. The cultivars were grouped into three clusters and the cultivars in Cluster-1 such as Prabhat, UniGreen NK41, Bisco 51, UniGreen UB100, Bharati 981 and Star Beej 7Star exhibited salt tolerance to a greater extent, accounting for higher STI in comparison to other cultivars grouped in Cluster-2 and Cluster-3. The high heritability (h2bs, >60%) and genetic advance (GAM, >20%) were recorded in 13 measured traits, indicating considerable genetic variations present in these traits. Therefore, using multivariate analysis based on the measured traits, six hybrid maize cultivars were selected as salt-tolerant and some traits such as Total Fresh Weight (TFW), Total Dry Weight (TDW), Total Na+, Total K+ contents and K+–Na+ Ratio could be effectively used for the selection criteria evaluating salt-tolerant maize genotypes at the early seedling stage.

Genome-wide association analysis of salt tolerance QTLs with SNP markers in maize (Zea mays L.)

2019 ◽  
Vol 41 (10) ◽  
pp. 1135-1145
Author(s):  
Yonghong Xie ◽  
Yan Feng ◽  
Qi Chen ◽  
Feike Zhao ◽  
Shuijuan Zhou ◽  
...  
Keyword(s):  
Zea Mays ◽  
Salt Tolerance ◽  
Association Analysis ◽  
Zea Mays L ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Genome Wide Association Analysis ◽  
Genome Wide

scholarly journals Association Analysis of Salt Tolerance in Asiatic cotton (Gossypium arboretum) with SNP Markers

2019 ◽  
Vol 20 (9) ◽  
pp. 2168 ◽  
Author(s):  
Tussipkan Dilnur ◽  
Zhen Peng ◽  
Zhaoe Pan ◽  
Koffi Palanga ◽  
Yinhua Jia ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Candidate Genes ◽  
Association Analysis ◽  
Association Studies ◽  
Snp Markers ◽  
Stem Length ◽  
Tolerance Index ◽  
Genome Wide Association Studies ◽  
Asiatic Cotton ◽  
Fundamental Information

Salinity is not only a major environmental factor which limits plant growth and productivity, but it has also become a worldwide problem. However, little is known about the genetic basis underlying salt tolerance in cotton. This study was carried out to identify marker-trait association signals of seven salt-tolerance-related traits and one salt tolerance index using association analysis for 215 accessions of Asiatic cotton. According to a comprehensive index of salt tolerance (CIST), 215 accessions were mainly categorized into four groups, and 11 accessions with high salinity tolerance were selected for breeding. Genome-wide association studies (GWAS) revealed nine SNP rich regions significantly associated with relative fresh weight (RFW), relative stem length (RSL), relative water content (RWC) and CIST. The nine SNP rich regions analysis revealed 143 polymorphisms that distributed 40 candidate genes and significantly associated with salt tolerance. Notably, two SNP rich regions on chromosome 7 were found to be significantly associated with two salinity related traits, RFW and RSL, by the threshold of −log10P ≥ 6.0, and two candidate genes (Cotton_A_37775 and Cotton_A_35901) related to two key SNPs (Ca7_33607751 and Ca7_77004962) were possibly associated with salt tolerance in G. arboreum. These can provide fundamental information which will be useful for future molecular breeding of cotton, in order to release novel salt tolerant cultivars.

scholarly journals Temporal salt stress-induced transcriptome alterations and regulatory mechanisms revealed by PacBio long-reads RNA sequencing in Gossypium hirsutum

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Delong Wang ◽  
Xuke Lu ◽  
Xiugui Chen ◽  
Shuai Wang ◽  
Junjuan Wang ◽  
...  
Keyword(s):  
Superoxide Dismutase ◽  
Salt Stress ◽  
Stress Response ◽  
Salt Tolerance ◽  
Gossypium Hirsutum ◽  
Stress Tolerance ◽  
Economic Losses ◽  
Salt Tolerant ◽  
Salt Stress Tolerance ◽  
Long Reads

Abstract Background Cotton (Gossypium hirsutum) is considered a fairly salt tolerant crop however, salinity can still cause significant economic losses by affecting the yield and deteriorating the fiber quality. We studied a salt-tolerant upland cotton cultivar under temporal salt stress to unfold the salt tolerance molecular mechanisms. Biochemical response to salt stress (400 mM) was measured at 0 h, 3 h, 12 h, 24 h and 48 h post stress intervals and single-molecule long-read sequencing technology from Pacific Biosciences (PacBio) combined with the unique molecular identifiers approach was used to identify differentially expressed genes (DEG). Results Antioxidant enzymes including, catalase (CAT), peroxidase (POD), superoxide dismutase (SOD) were found significantly induced under temporal salt stress, suggesting that reactive oxygen species scavenging antioxidant machinery is an essential component of salt tolerance mechanism in cotton. We identified a wealth of novel transcripts based on the PacBio long reads sequencing approach. Prolonged salt stress duration induces high number of DEGs. Significant numbers of DEGs were found under key terms related to stress pathways such as “response to oxidative stress”, “response to salt stress”, “response to water deprivation”, “cation transport”, “metal ion transport”, “superoxide dismutase”, and “reductase”. Key DEGs related to hormone (abscisic acid, ethylene and jasmonic acid) biosynthesis, ion homeostasis (CBL-interacting serine/threonine-protein kinase genes, calcium-binding proteins, potassium transporter genes, potassium channel genes, sodium/hydrogen exchanger or antiporter genes), antioxidant activity (POD, SOD, CAT, glutathione reductase), transcription factors (myeloblastosis, WRKY, Apetala 2) and cell wall modification were found highly active in response to salt stress in cotton. Expression fold change of these DEGs showed both positive and negative responses, highlighting the complex nature of salt stress tolerance mechanisms in cotton. Conclusion Collectively, this study provides a good insight into the regulatory mechanism under salt stress in cotton and lays the foundation for further improvement of salt stress tolerance.

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