Genetic basis and principal component analysis in cotton (Gossypium hirsutum L.) grown under water deficit condition.

Cotton is considered as the main crop in the agricultural sector of Pakistan. Water deficiency in this region in recent years has reduced the chances of high yields of cotton. Selection and creation of high-yielding varieties of cotton, even in water deficit conditions, is one of urgent tasks of today. For this purpose, 40 diverse genotypes of upland cotton were screened in normal and water deficit conditions in triplicate arrangement under split plot in a randomized complete block design. All the genotypes showed significant difference under both water regimes. Ten upland cotton accessions were screened out as water deficit tolerant (VH-144, IUB-212, MNH-886, VH-295, IR-3701, AA-802, NIAB-111, NS-121, FH-113, and FH-142) and five as water deficit sensitive (IR-3, CIM-443, FH-1000, MNH-147, and S-12) based on seed cotton yield and stress susceptibility index. These tolerant and sensitive genotypes were crossed in line × tester mating design. For further evaluation of genetic material, the seed of 50 F1 crosses and their 15 parents were field planted under normal and water deficit conditions during next cotton growing season. Traits related to yield under the study showed significant variations among the accessions and their half sibs. The results of the principal component analysis (PCA) exhibited that total variation exhibited by factors 1 and factor 2 were 55.55 and 41.95%, respectively. PCA transformed the variables into three factors, and only two factors (F1 and F2) had eigenvalue > 1. The degree of dominance revealed that all parameters were highly influenced by non-additive gene action under both water regimes. Furthermore, the line VH-295 and tester CIM-443 had better yield performance under water deficit stress. The cross-combinations, viz., VH-144 × S-12, NIAB-111 × IR-3, and VH-295 × MNH-147, were the best for yield contributing traits. These combinations may be helpful for germplasm enhancement on large scale under water scarcity. All the studied traits have non-additive types of gene action suggesting the usage of these genotypes in cotton hybrid development program against water deficit tolerance.

Unveiling the genetic architecture for lodging resistance in rice (Oryza sativa. L) by genome-wide association analyses.

Lodging is one of the major abiotic stresses, affecting the total crop yield and quality. The improved lodging resistance and its component traits potentially reduce the yield losses. The section modulus (SM), bending moment at breaking (M), pushing resistance (PR), and coefficient of lodging resistance (cLr) are the key elements to estimate the lodging resistance. Understanding the genetic architecture of lodging resistance-related traits will help to improve the culm strength and overall yield potential. In this study, a natural population of 795 globally diverse genotypes was further divided into two (indica and japonica) subpopulations and was used to evaluate the lodging resistance and culm strength-related traits. Significant diversity was observed among the studied traits. We carried out the genome-wide association evaluation of four lodging resistance traits with 3.3 million deep resolution single-nucleotide polymorphic (SNP) markers. The general linear model (GLM) and compressed mixed linear model (MLM) were used for the whole population and two subpopulation genome-wide association studies (GWAS), and a 1000-time permutation test was performed to remove the false positives. A total of 375 nonredundant QTLs were observed for four culm strength traits on 12 chromosomes of the rice genome. Then, 33 pleiotropic loci governing more than one trait were mined. A total of 4031 annotated genes were detected within the candidate genomic region of 33 pleiotropic loci. The functional annotations and metabolic pathway enrichment analysis showed cellular localization and transmembrane transport as the top gene ontological terms. The in silico and in vitro expression analyses were conducted to validate the three candidate genes in a pleiotropic QTL on chromosome 7. It validated OsFBA2 as a candidate gene to contribute to lodging resistance in rice. The haplotype analysis for the candidate gene revealed a significant functional variation in the promoter region. Validation and introgression of alleles that are beneficial to induce culm strength may be used in rice breeding for lodging resistance.

Conferring of drought tolerance in wheat (Triticum aestivum L.) genotypes using seedling indices.

Wheat is the most widely grown and consumed crop because of its economic and social benefits. This crop is more important globally for food and feed, and its productivity is particularly vulnerable to abiotic factors. In this study, 40 wheat genotypes were studied to access the drought tolerance level using completely randomized design (CRD) in 250 ml disposable cups through morpho-physiological attributes at seedling stage. The wheat germplasm was tested under normal and two drought stress level D1 (50% field capacity) and D2 (75% field capacity) for different seedling attributes such as germination percentage (GP), chlorophyll content (CC), shoot length (SL), root length (RL), shoot fresh weight (SFW), root fresh weight (RFW), seedling fresh weight (SDFW), shoot dry weight (SDW), root dry weight (RDW), relative water content (RWC), root/shoot ratio (RS), and seedling dry weight (SeDW). The results of analysis of variance (ANOVA) and spider analysis indicate that significant amount of genetic variation was present and behavior of studied germplasm showed different behavior in different environment. The correlation analysis showed that root length has significantly positive association with root/shoot ratio, dry weight, and fresh weight while negatively correlated with shoot length and relative water content. Based on the positively associated traits, the studied genetic material would improve genetic gain for drought tolerance. The multivariate analysis showed that out 13 principal components only five PCs were significant and has eigenvalue > 1, cumulatively showed 82.33, 83.07, and 97.34% of total variation under normal, D1 and D2 conditions, respectively. Significantly, the result of spider graph and multivariate analysis showed that genotypes G47, G48, G65, G68, and G80 performed well in all drought stress conditions and considered as drought-tolerant genotypes. The best performing genotypes can be used in future breeding programs. The selection on the bases of studied attributes is effective for development of drought-tolerant and high-yielding varieties for sustainable food security.

Characterization of wheat (Triticum aestivum L.) accessions using morpho-physiological traits under varying levels of salinity stress at seedling stage.

Abiotic stresses are the major stressors affecting wheat (Triticum aestivum L.) production worldwide. The world population is increasing continuously. It is very difficult to feed the population because one-third world's population consumes wheat as a staple food. Among all abiotic stresses, salinity is one that led to a drastic reduction in wheat crop fitness and productivity. Thus, understanding the effects of salinity stress becomes indispensable for wheat improvement programs which have depended mainly on the genetic variations present in the wheat genome through conventional breeding. Therefore, an experiment was conducted using a complete randomized design with four replications, to determine the selection criteria for salinity-tolerant germplasm based on morphophysiological traits at the seedling stage. Three levels of salt solutions, i.e., 4, 8, and 12 dSm-1 were applied and the performance of different genotypes under these three salinities levels was observed. Results depicted that leaf water content and relative water content were correlated with each other. Notably, selection based on these traits increased the performance of other characters. The genotypes G11, G13, G18, G22, and G36 performed best in the salinity stress. So, these genotypes are considered salinity-tolerant genotypes. The genotypes G4, G17, G19, G30, and G38 performed worst in the stress and these were salinity-susceptible genotypes. From the results of the principal component (PC) analysis, the first five PCs were indicated to have a substantial genetic variation from the total of 14 PCs. These PCs showed 75, 73, 65.324, and 65.162% of total variation under normal, salinity level 4, 8, and 12 dSm-1, respectively. Stomatal conductance, fresh shoot weight and fresh root weight, and dry shoot weight and dry root weight were not significant and negatively associated with all other traits studied, except for relative water and leaf water content. Overall, the results suggested that selection based on leaf water content and relative water content at the seedling stage would genetically improve salinity tolerance. Genotypes with good performance under salt stress conditions may be useful in future breeding programs and will be effective in developing high-yielding salt-tolerant wheat varieties.

Molecular characterization and validation of sunflower (Helianthus annuus L.) hybrids through SSR markers.

Genetic purity is a prerequisite for exploiting the potential of hybrids in cross-pollinated crops, such as sunflower. In this regard DNA-based study was conducted using 110 simple sequence repeat (SSR) markers to check the genetic purity of 23 parents and their 60 hybrids in sunflower. The polymorphism was shown in 92 markers with value 83.63%. The SSR markers ORS-453 and CO-306 showed the highest PIC values of 0.76 and 0.74, respectively. The primer ORS-453 amplified allele size of 310 base pairs (bp) for female parent L6 and 320 bp for L11, while for male parents, T1 and T2 had allele size 350 bp and 340 bp, respectively. The hybrids from these parents showed a similar size of alleles with parents, including hybrids L6×T1 (310 bp and 350 bp), L6×T2 (310 bp and 340 bp), and L11×T2 (320 bp and 340 bp). Similarly, the primer CO-306 amplified allele size 350 bp and 330 bp for female parents L6 and L11, respectively, while, allele size 300 bp and 310 bp for male parents T1 and T2, respectively. The hybrids' allele size was like the parents viz., L6×T1 (350 bp and 300 bp), L6×T2 (350 bp and 310 bp), and L11×T2 (330 bp and 310 bp). All 60 hybrids and their 23 parents were grouped into three main clusters (A, B and C) based upon DARWIN v.6.0 and STRUCTURE v.2.3 Bayesian analyses using genotypic data. Further, each main cluster was divided into two sub-divisions. Each sub-division showed the relatedness of parents and their hybrids, thus authenticating the genetic purity of hybrids. In conclusion, this study provides useful for accurate and effective identification of hybrids, which will help to improve seed genetic purity testing globally.

Genome-wide association mapping of bread wheat genotypes for sustainable food security and yield potential under limited water conditions.

Determining the genetic basis of yield and water deficient tolerance in wheat is vital for wheat breeding programs. Herein, a genome-wide association study (GWAS) was performed for water deficient and yield-related attributes on wheat genotypes with high-density Illumina 90K Infinium SNP array. Major yield and drought-related attributes were phenotyped on a panel of Pakistani and foreign accessions grown in non-stressed and water deficient stressed environments during two crop cycles. Among all accessions, highly significant variations were shown in studied environments for examined characters. Water deficient conditions, reduced the wheat yield and had strong and positive correlation among relative water content and grain yield per plant. Population structure analyses based on 90,000 SNP data, classify the accessions into 4 sub-populations. Marker-trait association analyses (MTA) revealed that 134 significant SNPs were linked with yield and drought tolerance attributes. Pleotropic loci RAC875_s117925_244 and RAC875_c16333_340 located on chromosome 5A and 2A respectively, were significantly linked with relative water contents (RWC), cell membrane thermo-stability (CMT), grain per spike (GPS), spikelet per spike (SPS) and grain yield per plant (GYP). The markers Ra_c58279_684, BobWhite_c23828_341 and IAAV3414 located on chromosomes 2A, 6B and 7B respectively, showed pleotropic effects for RWC, GPS and GYP under both environments. The current experiment not only validated several MTAs reported in other studies but also discovered novel MTAs which significant under drought-stressed conditions. A total of 171 candidate genes were recognized that could be cloned and functionally characterized for the respective associated traits. For RWC and CMT, total 11 and 3 associated SNPs were mapped on coding DNA sequence (CDS) of the identified candidate genes. Isolation and characterization of the candidate genes herein mapped SNPs will be useful in discovering novel genes underpinning drought tolerance in bread wheat to fulfill the wheat demand and sustainable food security under limited water conditions.

Genome-wide association mapping for high temperature tolerance in wheat through 90k SNP array using physiological and yield traits.

Dissecting the genetic basis of physiological and yield traits against tolerance to heat stress is an essential in wheat breeding programs to boost up the wheat yield for sustainable food security. Herein, a genome-wide association study (GWAS) was performed to reveal the genetic basis of heat tolerance using high-density Illumina 90K Infinium SNPs array through physiological and yield indices. These indices were phenotyped on a diverse panel of foreign and domestic genotypes of Pakistan, grown in normal and heat-stressed environments. Based on STRUCTURE analysis, the studied germplasm clustered into four sub-population. Highly significant variations with a range of moderate (58.3%) to high (77.8%) heritability was observed under both conditions. Strong positive correlation existed among physiological and yield related attributes. A total of 320 significant (-log10 P ≥ 3) marker-trait associations (MTAs) were identified for the observed characters. Out of them 169 and 151 MTAs were recorded in normal and heat stress environments, respectively. Among the MTA loci, three (RAC875_c103017_302, Tdurum_contig42087_1199, and Tdurum_contig46877_488 on chromosomes 4B, 6B, and 7B respectively), two (BobWhite_c836_422 and BS00010616_51) and three (Kukri_rep_c87210_361, D_GA8KES401BNLTU_253 and Tdurum_contig1015_131) on chromosomes 5A, 1B, and 3D at the positions 243.59cM, 77.82cM and 292.51cM) showed pleiotropic effects in studied traits under normal, heat-stressed and both conditions respectively. The present study not only authenticated the numerous previously reported MTAs for examined attributes but also revealed novel MTAs under heat-stressed conditions. Identified SNPs will be beneficial in determining the novel genes in wheat to develop the heat tolerant and best yielded genotypes to fulfill the wheat requirement for the growing population.

Genome-wide association mapping of bread wheat genotypes using yield and grain morphology-related traits under different environments.

Depleting water resources and increasing global temperature due to climate change are major challenges to agriculture and food security worldwide. Deciphering the underlying mechanisms of traits contributing to grain development and yield is essential for the development of climate-resilient cultivars. Therefore, this study assessed 105 bread wheat genotypes grown under control, drought, and heat-stress conditions for two crop seasons and performed a genome-wide association study (GWAS) using a 90k SNP array. The genotypes showed significant trait differences under all environmental conditions. Highly significant variation was observed, with moderate (50.09%) to high (76.19%) heritability in the studied germplasms. The studied traits were all also significantly positively correlated. A total of 541 significant associations (p ≤ 10-3) between marker and trait (MTAs) were observed after crossing the FDR <0.05 threshold for all traits. Among these, 195, 179, and 167 significant MTAs were detected under control, drought, and heat-stress conditions, respectively. Under the control and drought conditions, pleiotropic loci BS00010616_51 and BS00010868_51 were observed on chromosomes 7B and 1B situated at 186.24 cM and 35.47 cM, respectively. Pleiotropic loci BS00010868_51, Kukri_c11154_1723, and Ex_c10068_1509 were identified on chromosomes 1B, 5B, and 2A, respectively, under control and heat stress conditions. A stable and consistent locus (Excalibur_c20796_395) on chromosome 7A, located at 372.34 cM, was also linked to grain morphology and yield-related attributes in control, drought, and heat-stress conditions. The results of the current study confirmed several previously reported MTAs for the traits under consideration and identified new MTAs under harsh climatic conditions. These SNPs will aid in the discovery of novel genes in wheat. SNPs showing significant associations may be used in marker-assisted selection and allow the development of drought- and heat-tolerant genotypes with high yields to address global food security concerns.

Conferring drought-tolerant wheat genotypes through morpho-physiological and chlorophyll indices at seedling stage.

The decrease in water resources due to the excessive use of water for irrigation purpose and climatic changes represents a serious world-wide threat to food security. In this regards, 50 wheat accessions were analyzed, using completely random factorial design at the seedlings stage under normal and drought stress conditions. Significant variation was detected among all accessions under both conditions. All characters studied showed variations in the mean values in water deficit environments in studied gemplasm at seedling stage. As seedling fresh weight, dry weight, relative water content, cell membrane thermo-stability, chlorophyll a & b were positively associated among themselves under drought conditions which showed the significance of these attribute for water deficit areas in future wheat breeding programs. Based on their performance, five accessions namely Aas-11, Chakwal-86, Pasban-90, Chakwal-97 and Kohistan-97 were selected as drought tolerant and three accessions namely Mairaj-08, Lasani-2008 and Gomal-2008 were selected as drought susceptible genotypes. The choice of wheat accessions based on the characteristics of the seedlings is informal, low-priced and less hassle. Likewise, the seedlings attributes exhibit moderate to high variation with an additive genetics effects on the environments. Best performance accessions under water deficit environment will be beneficial in future wheat breeding schemes and early screening for the attributes suggested in current experiment will be useful for producing best-yielded and drought-tolerance wheat genotypes to sustainable food security.