Population structure and marker-trait association of salt tolerance in barley (Hordeum vulgare L.)

Molecular and agro-morphological characterization of new barley genotypes in arid environments

BACKGROUND

Genetic diversity, population structure, agro-morphological traits, and molecular characteristics, are crucial for either preserving genetic resources or developing new cultivars. Due to climate change, water availability for agricultural use is progressively diminishing. This study used 100 molecular markers (25 TRAP, 22 SRAP, 23 ISTR, and 30 SSR). Additionally, 15 morphological characteristics were utilized to evaluate the optimal agronomic traits of 12 different barley genotypes under arid conditions.

RESULTS

Substantial variations, ranging from significant to highly significant, were observed in the 15 agromorphological parameters evaluated among the 12 genotypes. The KSU-B101 barley genotype demonstrated superior performance in five specific traits: spike number per plant, 100-grain weight, spike number per square meter, harvest index, and grain yield. These results indicate its potential for achieving high yields in arid regions. The Sahrawy barley genotype exhibited the highest values across five parameters, namely leaf area, spike weight per plant, spike length, spike weight per square meter, and biological yield, making it a promising candidate for animal feed. The KSU-B105 genotype exhibited early maturity and a high grain count per spike, which reflects its early maturity and ability to produce a high number of grains per spike. This suggests its suitability for both animal feed and human food in arid areas. Based on marker data, the molecular study found that the similarity coefficients between the barley genotypes ranged from 0.48 to 0.80, with an average of 0.64. The dendrogram constructed from these data revealed three distinct clusters with a similarity coefficient of 0.80. Notably, the correlation between the dendrogram and its similarity matrix was high (0.903), indicating its accuracy in depicting the genetic relationships. The combined analysis revealed a moderate correlation between the morphological and molecular analysis, suggesting alignment between the two characterization methods.

CONCLUSIONS

The morphological and molecular analyses of the 12 barley genotypes in this study effectively revealed the varied genetic characteristics of their agro-performance in arid conditions. KSU-B101, Sahrawy, and KSU-B105 have emerged as promising candidates for different agricultural applications in arid regions. Further research on these genotypes could reveal their full potential for breeding programs.

Uncovering microsatellite markers associated with agronomic traits of South Sudan landrace maize

BACKGROUND

Maize has great importance in South Sudan as the most cultivated cereal after sorghum; however, numerous challenges are encountered in its production. To raise maize production, it is critical to exploit the wealth of its genetic variation for grain yield enhancement.

OBJECTIVE

This study aimed to conduct association analysis to identify specific simple sequence repeat (SSR) markers associated with quantitative agronomic traits.

METHODS

Genetic variation and population structure were investigated among 31 maize accessions by association analysis using 50 SSR markers and seven quantitative agronomic traits.

RESULTS

The genotypes exhibited abundant genetic variation, and 418 alleles were detected with an average of 8.4 alleles per locus. The average genetic diversity, major allele frequency, and polymorphic information content were 0.754, 0.373, and 0.725, respectively. The population structure based on 50 SSR markers divided the maize accessions into two main groups and an admixed group without considering their descent. Association analysis was performed using a general linear model (Q GLM) and a mixed linear model (Q + K MLM). Q GLM detected 44 trait-marker associations involving 23 SSR markers. Q + K MLM detected four marker-trait associations involving three SSR markers (umc2286, umc1303, umc1429) associated with days to tasseling, days to silking, leaf length, and leaf width.

CONCLUSIONS

The detected significant SSR markers related to agronomic traits could be useful for future genetic studies. Additionally, markers affecting several agronomic traits and overlapped SSR markers require further testing on a wide range of genotypes prior to their consideration as candidate markers for marker assisted selection for South Sudan maize improvement.

Genome-wide transcriptomic and functional analyses provide new insights into the response of spring barley to drought stress

Drought is a major abiotic stress that impairs the physiology and development of plants, ultimately leading to crop yield losses. Drought tolerance is a complex quantitative trait influenced by multiple genes and metabolic pathways. However, molecular intricacies and subsequent morphological and physiological changes in response to drought stress remain elusive. Herein, we combined morpho-physiological and comparative RNA-sequencing analyses to identify core drought-induced marker genes and regulatory networks in the barley cultivar 'Giza134'. Based on field trials, drought-induced declines occurred in crop growth rate, relative water content, leaf area duration, flag leaf area, concentration of chlorophyll (Chl) a, b and a + b, net photosynthesis, and yield components. In contrast, the Chl a/b ratio, stoma resistance, and proline concentration increased significantly. RNA-sequence analysis identified a total of 2462 differentially expressed genes (DEGs), of which 1555 were up-regulated and 907 were down-regulated in response to water-deficit stress (WD). Comparative transcriptomics analysis highlighted three unique metabolic pathways (carbohydrate metabolism, iron ion binding, and oxidoreductase activity) as containing genes differentially expressed that could mitigate water stress. Our results identified several drought-induced marker genes belonging to diverse physiochemical functions like chlorophyll concentration, photosynthesis, light harvesting, gibberellin biosynthetic, iron homeostasis as well as Cis-regulatory elements. These candidate genes can be utilized to identify gene-associated markers to develop drought-resilient barley cultivars over a short period of time. Our results provide new insights into the understanding of water stress response mechanisms in barley.

Association Analysis of Tiller-Related Traits with EST-SSR Markers in Psathyrostachys juncea

Psathyrostachys juncea is a long-lived perennial Gramineae grass with dense basal tillers and soft leaves. It is used widely in cold and dry areas of Eurasia and North America to establish grazing pasture and is even used as an ideal plant for revegetation and ecological restoration. Plant architecture, especially tillering traits, is critical for bunch grasses in breeding programs, and these traits in plants are mostly quantitative traits. In this study, the genetic diversity, population structure, and linkage disequilibrium of 480 individual lines were analyzed using 127 pairs of the EST-SSR marker, and a significant association between ten plant-architecture-related traits of P. juncea and molecular markers was found. The results of the genetic diversity analysis showed that the number of observed alleles was 1.957, the number of effective alleles was 1.682, Shannon's information index was 0.554, observed heterozygosity was 0.353, expected heterozygosity was 0.379, and the polymorphism information content was 0.300. A total of 480 individual lines were clustered into five groups based on population genetic structure, principal coordinate analysis, and unweighted pair group method with arithmetic mean analysis (UPGMA). The linkage disequilibrium coefficient (r2) was between 0.00 and 0.68, with an average of 0.04, which indicated a relatively low level of linkage disequilibrium among loci. The results of the association analysis revealed 55 significant marker-trait associations (MTA). Moreover, nine SSR markers were associated with multiple traits. This study provides tools with promising applications in the molecular selection and breeding of P. juncea germplasm.

Deciphering the genetic diversity and population structure of wild barley germplasm against corn leaf aphid, Rhopalosiphum maidis (Fitch)

Corn-leaf aphid (CLA-Rhopalosiphum maidis) is a major insect pest of barley (Hordeum vulgare) causing yield loss upto 30% under severe infestation. Keeping in view of the availability of very few sources of CLA resistance in barley, the present investigation was framed to assess the genetic diversity and population structure of 43 wild barley (H. vulgare subsp. spontaneum) genotypes using eight microsatellite markers against R. maidis. Three statistical methods viz. multivariate-hierarchical clustering, Bayesian clustering and PCoA, unanimously grouped genotypes into three subpopulations (K = 3) with 25.58% (SubPop1-Red), 39.53% (SubPop2-Green) and 34.88% (SubPop3-Blue) genotypes including admixtures. Based on Q ≥ 66.66%, 37.20% genotypes formed a superficial "Mixed/Admixture" subpopulation. All polymorphic SSR markers generated 36 alleles, averaging to 4.5 alleles/locus (2-7 range). The PIC and H were highest in MS31 and lowest in MS28, with averages of 0.66 and 0.71. MAF and mean genetic diversity were 0.16 and 89.28%, respectively. All these parameters indicated the presence of predominant genetic diversity and population structure amongst the studied genotypes. Based on AII, only 6 genotypes were found to be R. maidis resistant. SubPop3 had 91.66% (11) of the resistant or moderately resistant genotypes. SubPop3 also had the most pure genotypes (11), the least aphid infestation (8.78), and the highest GS (0.88), indicating its suitability for future R. maidis resistance breeding initiatives.

Genome-wide association analysis provides insights into the genetic basis of photosynthetic responses to low-temperature stress in spring barley

Low-temperature stress (LTS) is among the major abiotic stresses affecting the geographical distribution and productivity of the most important crops. Understanding the genetic basis of photosynthetic variation under cold stress is necessary for developing more climate-resilient barley cultivars. To that end, we investigated the ability of chlorophyll fluorescence parameters (F_VF_M, and F_VF₀) to respond to changes in the maximum quantum yield of Photosystem II photochemistry as an indicator of photosynthetic energy. A panel of 96 barley spring cultivars from different breeding zones of Canada was evaluated for chlorophyll fluorescence-related traits under cold acclimation and freeze shock stresses at different times. Genome-wide association studies (GWAS) were performed using a mixed linear model (MLM). We identified three major and putative genomic regions harboring 52 significant quantitative trait nucleotides (QTNs) on chromosomes 1H, 3H, and 6H for low-temperature tolerance. Functional annotation indicated several QTNs were either within the known or close to genes that play important roles in the photosynthetic metabolites such as abscisic acid (ABA) signaling, hydrolase activity, protein kinase, and transduction of environmental signal transduction at the posttranslational modification levels. These outcomes revealed that barley plants modified their gene expression profile in response to decreasing temperatures resulting in physiological and biochemical modifications. Cold tolerance could influence a long-term adaption of barley in many parts of the world. Since the degree and frequency of LTS vary considerably among production sites. Hence, these results could shed light on potential approaches for improving barley productivity under low-temperature stress.

Integrated GWAS and transcriptomic analysis reveal the candidate salt-responding genes regulating Na+/K+ balance in barley (Hordeum vulgare L.)

Salt stress is one of the main abiotic stresses affecting crop yield and quality. Barley has strong salt tolerance, however, the underlying genetic basis is not fully clear, especially in the seedling stage. This study examined the ionic changes in barley core germplasms under the control and salt conditions. Genome-wide association study (GWAS) analysis revealed 54 significant SNPs from a pool of 25,342 SNPs distributed in 7 chromosomes (Chr) of the Illumina Barley 50K SNP array. These SNPs are associated with ion homeostasis traits, sodium (Na⁺) and potassium (K⁺) content, and Na⁺/K⁺ ratio representing five genomic regions on Chr 2, 4, 5, 6, and 7 in the leaves of worldwide barley accessions. And there are 3 SNP peaks located on the Chr 4, 6, and 7, which could be the "hot spots" regions for mining and identifying candidate genes for salt tolerance. Furthermore, 616 unique candidate genes were screened surrounding the significant SNPs, which are associated with transport proteins, protein kinases, binding proteins, and other proteins of unknown function. Meanwhile, transcriptomic analysis (RNA-Seq) was carried out to compare the salt-tolerant (CM72) and salt-sensitive (Gairdner) genotypes subjected to salt stress. And there was a greater accumulation of differentially expressed genes(DEGs) in Gairdner compared to CM72, mainly enriched in metabolic pathway, biosynthesis of secondary metabolites, photosynthesis, signal transduction,emphasizing the different transcriptional response in both genotypes following salt exposure. Combined GWAS and RNA-Seq analysis revealed 5 promising salt-responding genes (PGK2, BASS3, SINAT2, AQP, and SYT3) from the hot spot regions, which were verified between the salt-tolerant and salt-sensitive varieties by qRT-PCR. In all, these results provide candidate SNPs and genes responsible for salinity responding in barley, and a new idea for studying such genetic basis in similar crops.

Genetic diversity and population structure assessment of Western Canadian barley cooperative trials

Studying the population structure and genetic diversity of historical datasets is a proposed use for association analysis. This is particularly important when the dataset contains traits that are time-consuming or costly to measure. A set of 96 elite barley genotypes, developed from eight breeding programs of the Western Canadian Cooperative Trials were used in the current study. Genetic diversity, allelic variation, and linkage disequilibrium (LD) were investigated using 5063 high-quality SNP markers via the Illumina 9K Barley Infinium iSelect SNP assay. The distribution of SNPs markers across the barley genome ranged from 449 markers on chromosome 1H to 1111 markers on chromosome 5H. The average polymorphism information content (PIC) per locus was 0.275 and ranged from 0.094 to 0.375. Bayesian clustering in STRUCTURE and principal coordinate analysis revealed that the populations are differentiated primarily due to the different breeding program origins and ear-row type into five subpopulations. Analysis of molecular variance based on PhiPT values suggested that high values of genetic diversity were observed within populations and accounted for 90% of the total variance. Subpopulation 5 exhibited the most diversity with the highest values of the diversity indices, which represent the breeding program gene pool of AFC, AAFRD, AU, and BARI. With increasing genetic distance, the LD values, expressed as r², declined to below the critical r^{2 =} 0.18 after 3.91 cM, and the same pattern was observed on each chromosome. Our results identified an important pattern of genetic diversity among the Canadian barley panel that was proposed to be representative of target breeding programs and may have important implications for association mapping in the future. This highlight, that efforts to identify novel variability underlying this diversity may present practical breeding opportunities to develop new barley genotypes.

Breeding of Vegetable Cowpea for Nutrition and Climate Resilience in Sub-Saharan Africa: Progress, Opportunities, and Challenges

Currently, the world population is increasing, and humanity is facing food and nutritional scarcity. Climate change and variability are a major threat to global food and nutritional security, reducing crop productivity in the tropical and subtropical regions of the globe. Cowpea has the potential to make a significant contribution to global food and nutritional security. In addition, it can be part of a sustainable food system, being a genetic resource for future crop improvement, contributing to resilience and improving agricultural sustainability under climate change conditions. In malnutrition prone regions of sub-Saharan Africa (SSA) countries, cowpea has become a strategic dryland legume crop for addressing food insecurity and malnutrition. Therefore, this review aims to assess the contribution of cowpea to SSA countries as a climate-resilient crop and the existing production challenges and perspectives. Cowpea leaves and immature pods are rich in diverse nutrients, with high levels of protein, vitamins, macro and micronutrients, minerals, fiber, and carbohydrates compared to its grain. In addition, cowpea is truly a multifunctional crop for maintaining good health and for reducing non-communicable human diseases. However, as a leafy vegetable, cowpea has not been researched and promoted sufficiently because it has not been promoted as a food security crop due to its low yield potential, susceptibility to biotic and abiotic stresses, quality assurance issues, policy regulation, and cultural beliefs (it is considered a livestock feed). The development of superior cowpea as a leafy vegetable can be approached in different ways, such as conventional breeding and gene stacking, speed breeding, mutation breeding, space breeding, demand-led breeding, a pan-omics approach, and local government policies. The successful breeding of cowpea genotypes that are high-yielding with a good nutritional value as well as having resistance to biotics and tolerant to abiotic stress could also be used to address food security and malnutrition-related challenges in sub-Saharan Africa.

QTL Mapping and Phenotypic Variation for Seedling Vigour Traits in Barley (Hordeum vulgare L.)

Seed vigour is considered a critical stage for barley production, and cultivars with early seedling vigour (ESV) facilitate rapid canopy formation. In this study, QTLs for 12 ESV-related traits were mapped using 185 RILs derived from a Xena x H94061120 evaluated across six independent environments. DArT markers were used to develop a genetic map (1075.1 cM; centimorgans) with an average adjacent-marker distance of 3.28 cM. In total, 46 significant QTLs for ESV-related traits were detected. Fourteen QTLs for biomass yield were found on all chromosomes, two of them co-localized with QTLs on 1H for grain yield. The related traits: length of the first and second leaves and dry weight of the second leaf, biomass yield and grain yield, had high heritability (>30%). Meanwhile, a significant correlation was observed between grain yield and biomass yield, which provided a clear image of these traits in the selection process. Our results demonstrate that a pleiotropic QTL related to the specific leaf area of the second leaf, biomass yield, and grain yield was linked to the DArT markers bPb-9280 and bPb-9108 on 1H, which could be used to significantly improve seed vigour by marker-assisted selection and facilitate future map-based cloning efforts.

Detailed Genetic Analysis for Identifying QTLs Associated with Drought Tolerance at Seed Germination and Seedling Stages in Barley

Drought induces several challenges for plant development, growth, and production. These challenges become more severe, in particular, in arid and semiarid countries like Egypt. In terms of production, barley ranks fourth after wheat, maize, and rice. Seed germination and seedling stages are critical stages for plant establishment and growth. In the current study, 60 diverse barley genotypes were tested for drought tolerance using two different treatments: control (0-PEG) and drought (20%-PEG). Twenty-two traits were estimated for seed germination and seedling parameters. All traits were reduced under drought stress, and a significant variation was found among genotypes under control and stress conditions. The broad-sense heritability estimates were very high under both control and drought for all traits. It ranged from 0.63 to 0.97 under the control condition and from 0.89 to 0.97 under drought, respectively. These high heritabilities suggested that genetic improvement of drought tolerance in barley at both stages is feasible. The principal component analysis revealed that root-related parameters account for the largest portion of phenotypic variation in this collection. The single-marker analysis (SMA) resulted in 71 quantitative trait loci (QTLs) distributed across the seven chromosomes of barley. Thirty-three QTLs were detected for root-length-related traits. Many hotspots of QTLs were detected for various traits. Interestingly, some markers controlled many traits in a pleiotropic manner; thus, they can be used to control multiple traits at a time. Some QTLs were constitutive, i.e., they are mapped under control and drought, and targeting these QTLs makes the selection for drought tolerance a single-step process. The results of gene annotation analysis revealed very potential candidate genes that can be targeted to select for drought tolerance.

Marker-trait association for grain weight of spring barley in well-watered and drought environments

Climate change will increase the effect of drought stress which is one of major constrains for barley production and productivity in Egypt. Identification and development new cultivars having a high drought tolerance combined with a high yield are urgently needed. In this study, a set of 60 highly homozygous and diverse barley genotypes was evaluated in well-watered (N) and dry (D) environments for two successive seasons. Five yield traits were scored; plant height, spike length, days to flowering, grain yield per spike (GYPS), and thousand kernel weight (TKW). High genetic variation was found among genotypes in all studied traits under N and D. High heritability for all traits was observed in both seasons. The drought susceptibility index (DSI) for GYPS and TKW was estimated to determine the tolerant and susceptible genotypes in both seasons. As a result, four spring barley genotypes were considered drought tolerant for TKW and GYPS in both seasons. A set of ten single sequence repeats primers, developed from wheat genome, were tested in the 60 genotypes. All SSR primers had a high polymorphism among the genotypes producing 82 marker alleles. Single marker analysis was performed for DSI, TKW, and GYPS in both seasons. Twenty QTLs were found to be associated with low DSI and high GYPS and TKW in N and D. The marker alleles associated with the 20 QTL were screened in the four tolerant genotypes. PNBYT15 included only one marker allele associated with one QTL, while, SCYT-28 included six marker alleles controlling nine QTL. The high genetic variation and heritability for the studied traits indicated that these traits could be used for selection for high yielding and drought tolerance. The four drought tolerant genotypes can be used for a further breeding program to improve drought tolerance in barley.

Genetic diversity and genetic variation in morpho-physiological traits to improve heat tolerance in Spring barley

Heat stress is one of the abiotic stresses that limit the production and productivity of barley. Understanding the genetic variation, changes in physiological processes and level of genetic diversity existing among genotypes are needed to produce new cultivars not only having a high tolerance to heat stress, but also displaying high yield. To address this challenge, a set of 60 highly homozygous, diverse barley genotypes were evaluated under normal and heat stress conditions in two seasons of 2014/2015 and 2015/2016. Seedling vigor (SV) as a morphological trait was visually scored under normal conditions. Plant height (Ph), days to flowering (DOF), 1000-kernel weight (TKW), grain yield per spike (GYPS), yield per plot (YPP) and biological yield (BY) were measured. Moreover, proline content (ProC), soluble carbohydrate content (SCC), starch content, soluble protein (SP), and amino acid (AA) content as physiological parameters were analyzed from the grains. High genetic variation was observed among genotypes for all traits scored in this study. All traits had high broad-sense heritability estimates ranging from 0.59 (SV) to 0.97 (TKW) for yield traits. Seedling vigor was significantly correlated with all yield traits under both conditions. Among all physiological traits, the increase in ProC and reduction in starch content due to heat stress had significant correlations with the reduction due to heat stress in YPP, GYPS, TKW, and BY. Furthermore, the genetic diversity based on genetic distance (GD) among genotypes was investigated using 206 highly polymorphic SSR marker alleles. The GD ranged from 0.70 to 0.98 indicating that these genotypes are highly and genetically dissimilar. The combination of analyses using molecular markers, genetic variation in yield traits, and changes in physiological traits provided useful information in identifying the tolerant genotypes which can be used to improve heat tolerance in barley through breeding.

Association analysis of salt tolerance in cowpea (Vigna unguiculata (L.) Walp) at germination and seedling stages

This is the first report on association analysis of salt tolerance and identification of SNP markers associated with salt tolerance in cowpea. Cowpea (Vigna unguiculata (L.) Walp) is one of the most important cultivated legumes in Africa. The worldwide annual production in cowpea dry seed is 5.4 million metric tons. However, cowpea is unfavorably affected by salinity stress at germination and seedling stages, which is exacerbated by the effects of climate change. The lack of knowledge on the genetic underlying salt tolerance in cowpea limits the establishment of a breeding strategy for developing salt-tolerant cowpea cultivars. The objectives of this study were to conduct association mapping for salt tolerance at germination and seedling stages and to identify SNP markers associated with salt tolerance in cowpea. We analyzed the salt tolerance index of 116 and 155 cowpea accessions at germination and seedling stages, respectively. A total of 1049 SNPs postulated from genotyping-by-sequencing were used for association analysis. Population structure was inferred using Structure 2.3.4; K optimal was determined using Structure Harvester. TASSEL 5, GAPIT, and FarmCPU involving three models such as single marker regression, general linear model, and mixed linear model were used for the association study. Substantial variation in salt tolerance index for germination rate, plant height reduction, fresh and dry shoot biomass reduction, foliar leaf injury, and inhibition of the first trifoliate leaf was observed. The cowpea accessions were structured into two subpopulations. Three SNPs, Scaffold87490_622, Scaffold87490_630, and C35017374_128 were highly associated with salt tolerance at germination stage. Seven SNPs, Scaffold93827_270, Scaffold68489_600, Scaffold87490_633, Scaffold87490_640, Scaffold82042_3387, C35069468_1916, and Scaffold93942_1089 were found to be associated with salt tolerance at seedling stage. The SNP markers were consistent across the three models and could be used as a tool to select salt-tolerant lines for breeding improved cowpea tolerance to salinity.