scholarly journals Identification of genomic regions associated with agronomical traits of bread wheat under two levels of salinity using GWAS

2021 ◽  
Author(s):  
Fahad Alotaibi ◽  
Rahmah N. Al-Qthanin ◽  
Maha Aljabri ◽  
Mohammed Albaqami ◽  
Salah Abou-Elwafa
Keyword(s):  
Salt Stress ◽  
Agronomic Traits ◽  
Snp Markers ◽  
Yield Potential ◽  
Stress Index ◽  
Phenotypic Trait ◽  
Phenotypic Traits ◽  
Tolerance Index ◽  
Accurate Identification ◽  
Agronomical Traits

Abstract Soil salinity is a major environmental stress that adversely impacts the growth, development, productivity and quality of crop species, in particular, in arid and semi-arid regions. Identification of chromosomal regions associated with agronomic traits under salinity stress is crucial for improving salinity tolerance in wheat. GWAS and structure analyses were employed to evaluate 289 elite lines of the Wheat Association Mapping Initiative (WAMI) population under low (LS) and high (HS) salinity conditions using 15,737 SNP markers and seven agronomical traits. Evaluated genotypes responded differently to the different environments in all measured phenotypic traits, highlighting genetic diversity within the WAMI population in response to salt stress. Heritability degree ranged from moderate (37%) to high (88%). GWAS identified 118 and 120 significant associations between SNP markers and seven evaluated phenotypic traits under LS and HS conditions, respectively. Significant association of some markers with more than one phenotypic trait was observed, indicating possible pleiotropic or indirect effects. A high degree of significant linkage disequilibrium (> 52%) was observed among SNP markers on different chromosomes indicating epistatic interaction. The salt stress index (STI) exhibited a positive significant correlation to grain yield per plant (GYP) under both LS and HS conditions (R2 = 0.851–0.856). A linear regression between STI and GYP under HS conditions (GYPs) was identified, suggest that STI is the best tolerance index for predicting high yielding-genotypes. The results present the WAMI population as a valuable source for improving yield potential for salt tolerance in wheat. Furthermore, our findings emphasize that GWAS is a powerful tool in promoting wheat breeding through accurate identification of molecular markers significantly associated with agronomic traits, which is essential for marker-assisted breeding.

scholarly journals Assessment of the genetic diversity and population structure of groundnut germplasm collections using phenotypic traits and SNP markers: Implications for drought tolerance breeding

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259883
Author(s):  
Seltene Abady ◽  
Hussein Shimelis ◽  
Pasupuleti Janila ◽  
Shasidhar Yaduru ◽  
Admire I. T. Shayanowako ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Drought Tolerance ◽  
Agronomic Traits ◽  
Snp Markers ◽  
Phenotypic Traits ◽  
Environment Interaction ◽  
Optimum Conditions ◽  
Pod Yield ◽  
Germplasm Collections

Profiling the genetic composition and relationships among groundnut germplasm collections is essential for the breeding of new cultivars. The objectives of this study were to assess the genetic diversity and population structure among 100 improved groundnut genotypes using agronomic traits and high-density single nucleotide polymorphism (SNP) markers. The genotypes were evaluated for agronomic traits and drought tolerance at the International Crop Research Institute for the Semi-Arid Tropics (ICRISAT)/India across two seasons. Ninety-nine of the test genotypes were profiled with 16363 SNP markers. Pod yield per plant (PY), seed yield per plant (SY), and harvest index (HI) were significantly (p < 0.05) affected by genotype × environment interaction effects. Genotypes ICGV 07222, ICGV 06040, ICGV 01260, ICGV 15083, ICGV 10143, ICGV 03042, ICGV 06039, ICGV 14001, ICGV 11380, and ICGV 13200 ranked top in terms of pod yield under both drought-stressed and optimum conditions. PY exhibited a significant (p ≤ 0.05) correlation with SY, HI, and total biomass (TBM) under both test conditions. Based on the principal component (PC) analysis, PY, SY, HSW, shelling percentage (SHP), and HI were allocated in PC 1 and contributed to the maximum variability for yield under the two water regimes. Hence, selecting these traits could be successful for screening groundnut genotypes under drought-stressed and optimum conditions. The model-based population structure analysis grouped the studied genotypes into three sub-populations. Dendrogram for phenotypic and genotypic also grouped the studied 99 genotypes into three heterogeneous clusters. Analysis of molecular variance revealed that 98% of the total genetic variation was attributed to individuals, while only 2% of the total variance was due to variation among the subspecies. The genetic distance between the Spanish bunch and Virginia bunch types ranged from 0.11 to 0.52. The genotypes ICGV 13189, ICGV 95111, ICGV 14421, and ICGV 171007 were selected for further breeding based on their wide genetic divergence. Data presented in this study will guide groundnut cultivar development emphasizing economic traits and adaptation to water-limited agro-ecologies, including in Ethiopia.

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.

scholarly journals Agronomical, physiological and molecular evaluation reveals superior salt-tolerance in bread wheat through salt-induced priming approach

2021 ◽  
Vol 49 (2) ◽  
pp. 12310
Author(s):  
Othman ALZAHRANI ◽  
Heba ABOUSEADAA ◽  
Taghreed K. ABDELMONEIM ◽  
Mohammed A. ALSHEHRI ◽  
Mohamed EL-MOGY ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Agronomic Traits ◽  
Ion Homeostasis ◽  
Crop Productivity ◽  
Vital Role ◽  
Wheat Crop ◽  
Pretreated Group ◽  
Mda Content ◽  
Agronomical Traits

Salt stress significantly limit wheat crop productivity worldwide. Exposure to non-lethal levels of salt stress, referred to as "salt-priming", allows plants to persist subsequent lethal conditions; the priming effect continues even after an extended salt stress-free period. This study attempted to evaluate the effectiveness of the salt-induced priming approach to cope with the toxic effects of long-term salinity stress in wheat. After 22 days of gradual salt acclamation to reach 250 mM NaCl, plants were recovered for eight days and finally shocked with 250 mM NaCl (priming+shock) for 7 days. After that, physiological parameters and gene expression of six salt-responsive genes were assessed. Additionally, 120 days after germination (at the end of the season), agronomic traits were recorded. Analysis of the agronomical traits revealed higher productivity in the salt-pretreated group (priming+shock) plants than the non-pretreated (shock only). Consistently, salt-pretreated plants maintained higher photosynthetic pigments level and decreased proline and MDA content than non-pretreated, suggesting enhanced salt tolerance. Moreover, salt-pretreated plants sustained high expressional levels of salt-responsive genes (TaNHX1, TaSOS1, TaSOS4, TaHKT1, TaHKT2, and TaAKT1) comparing with non-pretreated, indicating a vital role in ion homeostasis and conferring salt tolerance. Ultimately, this finding could facilitate novel smart approaches to improve wheat productivity under salt stress.

scholarly journals Regions of Chromosome 2A of Bread Wheat (Triticum aestivum L.) Associated with Variation in Physiological and Agronomical Traits under Contrasting Water Regimes

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1023
Author(s):  
Tatyana A. Pshenichnikova ◽  
Svetlana V. Osipova ◽  
Olga G. Smirnova ◽  
Irina N. Leonova ◽  
Marina D. Permyakova ◽  
...  
Keyword(s):  
Water Supply ◽  
Candidate Genes ◽  
Gene Networks ◽  
Agronomic Traits ◽  
Negative Impact ◽  
Critical Role ◽  
Wheat Yield ◽  
Snp Markers ◽  
Single Chromosome ◽  
Agronomical Traits

Understanding the genetic architecture of drought tolerance is of great importance for overcoming the negative impact of drought on wheat yield. Earlier, we discovered the critical role of chromosome 2A for the drought-tolerant status of wheat spring cultivar Saratovskaya 29. A set of 92 single-chromosome recombinant double haploid (SCRDH) lines were obtained in the genetic background of Saratovskaya 29. The lines carry fragments of chromosome 2A from the drought-sensitive cultivar Yanetzkis Probat. The SCRDH lines were used to identify regions on chromosome 2A associated with the manifestation of physiological and agronomical traits under distinct water supply, and to identify candidate genes that may be associated with adaptive gene networks in wheat. Genotyping was done with Illumina Infinium 15k wheat array using 590 SNP markers with 146 markers being polymorphic. In four identified regions of chromosome 2A, 53 out of 58 QTLs associated with physiological and agronomic traits under contrasting water supply were mapped. Thirty-nine candidate genes were identified, of which 18 were transcription factors. The region 73.8–78.1 cM included the largest number of QTLs and candidate genes. The variation in SNPs associated with agronomical and physiological traits revealed among the SCRDH lines may provide useful information for drought related marker-assisted breeding.

scholarly journals Identification of genetic loci associated with major agronomic traits of wheat (Triticum aestivum L.) based on genome-wide association analysis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Woo Joo Jung ◽  
Yong Jin Lee ◽  
Chon-Sik Kang ◽  
Yong Weon Seo
Keyword(s):  
Triticum Aestivum ◽  
Candidate Genes ◽  
Agronomic Traits ◽  
Genome Wide Association ◽  
Stem Length ◽  
Phenotypic Trait ◽  
Phenotypic Traits ◽  
Genetic Loci ◽  
Genome Wide ◽  
Population Structure Analysis

Abstract Background Bread wheat (Triticum aestivum L.) is one of the most widely consumed cereal crops, but its complex genome makes it difficult to investigate the genetic effect on important agronomic traits. Genome-wide association (GWA) analysis is a useful method to identify genetic loci controlling complex phenotypic traits. With the RNA-sequencing based gene expression analysis, putative candidate genes governing important agronomic trait can be suggested and also molecular markers can be developed. Results We observed major quantitative agronomic traits of wheat; the winter survival rate (WSR), days to heading (DTH), days to maturity (DTM), stem length (SL), spike length (SPL), awn length (AL), liter weight (LW), thousand kernel weight (TKW), and the number of seeds per spike (SPS), of 287 wheat accessions from diverse country origins. A significant correlation was observed between the observed traits, and the wheat genotypes were divided into three subpopulations according to the population structure analysis. The best linear unbiased prediction (BLUP) values of the genotypic effect for each trait under different environments were predicted, and these were used for GWA analysis based on a mixed linear model (MLM). A total of 254 highly significant marker-trait associations (MTAs) were identified, and 28 candidate genes closely located to the significant markers were predicted by searching the wheat reference genome and RNAseq data. Further, it was shown that the phenotypic traits were significantly affected by the accumulation of favorable or unfavorable alleles. Conclusions From this study, newly identified MTA and putative agronomically useful genes will help to study molecular mechanism of each phenotypic trait. Further, the agronomically favorable alleles found in this study can be used to develop wheats with superior agronomic traits.

scholarly journals Genetic analysis of agronomical traits in recombinant inbred lines of cowpea (Vignaunguiculata(L.) Walp.)under two water regimes.

2015 ◽  
Vol 5 (1) ◽  
pp. 578-590
Author(s):  
Charlotte TONESSIA ◽  
N'Dri KOUASSI ◽  
Ndiaga CISSE ◽  
Severin Aké
Keyword(s):  
Genetic Variation ◽  
Recombinant Inbred ◽  
Agronomic Traits ◽  
Average Distance ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Snp Markers ◽  
Linkage Groups ◽  
Water Regimes ◽  
Agronomical Traits

Single nucleotide polymorphism (SNP) markers were used to develop a genetic-linkage map and to identify QTLsinvolved in the genetic variation of agronomical traits in cowpeaunder two water regimes. A total of 1536 SNP GoldenGate assay were used to screen for polymorphism in a cowpea population of recombinant inbred lines. A total of 299 SNP markers amplified polymorphic products of which 228 mapped to the 11 cowpea linkage groups with an average distance of 6.5 cM between markers. The new SNP genetic map with a total length of 1281,8 cM were aligned with the consensus cowpea map allowing filling some gaps, which will increase QTLs analysis. A total of 31 QTLs affecting agronomic traits were identified and mapped to cowpea genomic regions. Among them 45% explaining from 3 to 35% of genetic variation were detected for both water conditions. Co-locations between QTLs were identified on several linkage groups among them QTLs affecting harvest index (HI) and grain yield suggesting their common genetic bases. Because, HI has been shown as the most stable and highly correlated parameter with cowpea yield under stress; our results will enable the efficiency of MAS and enhance genetic progress in cowpea.

Evaluation of Agronomic Traits of Sponge Gourd (Luffa cylindrica) Inbred Lines Under Plastic House in Thua Thien Hue

2017 ◽  
Vol 126 (3E) ◽  
Author(s):  
Trương Thị Hồng Hải ◽  
Nguyễn Thị Diệu Thể ◽  
Phan Thu Thảo
Keyword(s):  
Skin Color ◽  
Agronomic Traits ◽  
Block Design ◽  
Leaf Traits ◽  
Pure Line ◽  
Inbred Lines ◽  
Fruit Shape ◽  
Yield Potential ◽  
High Yield ◽  
Sponge Gourd

In order to establish the pure line of sponge gourd containing aroma feature, we selected the desirable inbred lines by using a self-pollinating method. The present study was investigated to estimate the morphological traits and fruit quality of 6 sponge gourd inbred lines which generated at 4th generation of an aroma Luffa accession B29 under plastic house conditions. The experiment was conducted in a randomized complete block design (RCBD) with three replications, from May to November in 2016. Five plants per replication were examined. The results indicated that all inbred lines could grow well under plastic house conditions. The inbred lines had the same stem and leaf traits; whereas fruit shape, skin color and fruit veins color were observed differently among inbred lines. The aromatic trait was retained in all inbred lines either before or after cooking. The high yield was found in lines BC1 and BC2 by 10.1 tons/ha and 10.7 tons/ha, respectively. These inbred lines should be examined in open field condition to confirm the presence of aromatic trait and yield potential before completion of the procedures for recognition of new Luffa varieties.  

scholarly journals Normal approximation for mixtures of normal distributions and the evolution of phenotypic traits

2021 ◽  
Vol 53 (1) ◽  
pp. 162-188
Author(s):  
Krzysztof Bartoszek ◽  
Torkel Erhardsson
Keyword(s):  
Normal Distribution ◽  
Phenotypic Trait ◽  
Phenotypic Traits ◽  
Normal Distributions ◽  
Average Value ◽  
Conditional Moments ◽  
Mixture Of Normal Distributions ◽  
Explicit Bounds ◽  
Mixtures Of Normal Distributions ◽  
Parameter Values

AbstractExplicit bounds are given for the Kolmogorov and Wasserstein distances between a mixture of normal distributions, by which we mean that the conditional distribution given some $\sigma$ -algebra is normal, and a normal distribution with properly chosen parameter values. The bounds depend only on the first two moments of the first two conditional moments given the $\sigma$ -algebra. The proof is based on Stein’s method. As an application, we consider the Yule–Ornstein–Uhlenbeck model, used in the field of phylogenetic comparative methods. We obtain bounds for both distances between the distribution of the average value of a phenotypic trait over n related species, and a normal distribution. The bounds imply and extend earlier limit theorems by Bartoszek and Sagitov.

scholarly journals Evaluating Genotype × Environment Interactions of Yield Traits and Adaptability in Rice Cultivars Grown under Temperate, Subtropical and Tropical Environments

Agriculture ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 558
Author(s):  
Xing Huang ◽  
Su Jang ◽  
Backki Kim ◽  
Zhongze Piao ◽  
Edilberto Redona ◽  
...  
Keyword(s):  
Yield Component ◽  
Yield Potential ◽  
High Yield ◽  
Environment Interaction ◽  
Accurate Identification ◽  
Rice Varieties ◽  
Panicle Number ◽  
Tropical Conditions ◽  
Component Traits ◽  
Yield Component Traits

Rice yield is a complex trait that is strongly affected by environment and genotype × environment interaction (GEI) effects. Consideration of GEI in diverse environments facilitates the accurate identification of optimal genotypes with high yield performance, which are adaptable to specific or diverse environments. In this study, multiple environment trials were conducted to evaluate grain yield (GY) and four yield-component traits: panicle length, panicle number, spikelet number per panicle, and thousand-grain weight. Eighty-nine rice varieties were cultivated in temperate, subtropical, and tropical regions for two years. The effects of both GEI (12.4–19.6%) and environment (23.6–69.6%) significantly contributed to the variation of all yield-component traits. In addition, 37.1% of GY variation was explained by GEI, indicating that GY performance was strongly affected by the different environmental conditions. GY performance and genotype stability were evaluated using simultaneous selection indexing, and 19 desirable genotypes were identified with high productivity and broad adaptability across temperate, subtropical, and tropical conditions. These optimal genotypes could be recommended for cultivation and as elite parents for rice breeding programs to improve yield potential and general adaptability to climates.

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