Hafiz Ghulam Muhu-Din Ahmed's research while affiliated with The Islamia University of Bahawalpur and other places

Rice is an important staple food crop, but in many countries, average rice yields are much lower than their yield potential. The objective of the present study was to evaluate the phenotypic performance of diverse rice genotypes (310) for yield traits, identify high-yielding early-duration genotypes with greater partitioning efficiency, and classify the best and worst genotypes based on their performance in the 2019−20 growing season under randomized complete block design (RCBD) with three replications. The analysis of variance showed significant differences for all the traits between genotypes (p ≤ 0.001). Correlation analysis revealed a significant correlation between grain yield plant −1 and flag leaf area, panicle grain weight, panicle length, number of spikelets panicle −1, spikelet fertility, number of grains panicle −1, 1000 grain weight, grain length, net photosynthesis, and water use efficiencies. Principal component analysis indicated genetic variation between all genotypes. The cumulative genetic variation in the first two principal components (PCs) was 69.18% (PC 1: 57.74% and PC 2: 11.44%). PC 1 added more toward yield and related traits to the separation of rice genotypes and contributed to the variability for 1000 grain weight (7.74%), spikelet fertility (7.56%), number of spikelets panicle −1 (7.54%), flag leaf area (7.41%), and shoot dry weight (7.13%). Projection in biplot analysis confirmed that all the best genotypes were opposite to only the worst genotype G-19 and all others were positively associated with each other. Thus, the selection of these traits which are positively related to grain yield, and the selection of best genotypes in rice would be useful for improving yield. Diversity and association of physiological and yield-related traits could be useful to improve crops through the selection of useful traits to increase productivity and meet the demands of the growing population.

Rice is the principal cash crop of Pakistan, however, its yield is severely affected by salinity. In arid and coastal areas of rice cultivation, salinity is one of the major factors that affect its yield. In present study genetic variability and correlation analysis between different morpho-physiological traits at the seedling stage of various rice genotypes were studied. The experiment was design in a completely Random Design with three replications. At the seedling stage, rice seedlings were treated with two sodium chloride concentrations and various morphological and physiological parameters were investigated. For all of the traits analysis of variance revealed significant differences among the genotypes. Correlation analysis showed that under normal conditions, most of the studied traits had significant positive correlations with each other except root dry weight and relative water contents. While in T1, most traits had significant positive correlation with each other, however in T2, correlation of some of the traits was significantly positive while few traits showed significantly negative correlations with each other. From the results, it was found that seedlings treated with 50 and 200 mM salt solutions were smaller than the control; however, secondary leaves developed in them. Seedlings treated with 50 and 200 mM salt solutions could not progress toward secondary leaves. Under salt stress, lower fresh weight of seedlings was found then normal seedlings. With salt treatments, the chlorophyll contents of seedlings decreased significantly. Out of nine principal components (PCs), the first two PCs showed significant genetic variation under normal and salinity conditions. The first two PCs under normal, T1 and T2showed 81%, 84% and 71% total variation respectively in the studied genotypes. From the analysis, it was found that traits such as root length, root fresh and dry weight, chlorophyll contents and stomatal conductance at the seedling stage would be useful criteria for genetic improvement. As compared to white rice, pigmented rice, results suggested that studied pigmented genotypes could be beneficial for further study of salinity effects on growth processes, morpho-physiological concerns and advanced stages of growth, since the salinity tolerance of a crop at germination and early seedling stage may not parallel to advanced stage. Future pigmented rice breeding programs may benefit from outperforming genotypes under salt stress conditions and early selection for the features suggested in this work may prove to be successful in creating high-yielding and salinity-tolerant rice varieties.

Because of the variety of genetic components, plants are affected by complex genetic-environment-management interactions that drive phenotypic plasticity. Reliable, automatic, multifunctional, and high-throughput phenotypic technology are more taken into consideration as crucial tools for the speedy development of genetic gain in breeding schemes. With the rapid advancement in high-throughput phenotyping (HTP) technology, a study in this aspect is ingoing a novel era called “phenomics.” The crop phenotyping network now no longer most effective needs to construct a multi-domain, multilevel, and multiscale crop phenotyping large database however additionally to analyze technical structures for phenotypic developments identity and increase bioinformatics technology for statistics extraction from the overpowering quantities of omics data. HTP platforms can monitor phenotypic variation in plants using red, green, and blue (RGB) cameras, hyperspectral sensors, and computed tomography are examples of sensors that can be linked to environmental and genotypic data. Since whole-genome sequencing (WGS) and next-generation sequencing (NGS) of many crops has been achieved, functional genomic studies of crops have divided into the main data and the high-throughput era. However, obtaining large-scale phenotypic data has become one of the most significant roadblocks to crop breeding and functional genomics research. Phenomics can give vast amounts of phenotypic data at a minimal cost because it is an inherently big scale and high throughput. Obtaining high-quality digital phenotypic data with detailed information (e.g., descriptions of protocols, growth conditions, etc., in a standardized format) allows for the examination and quantitative modeling of molecular networks influencing complex features including development, stress tolerance, and metabolism as well as community relationships. In this chapter, we will discuss how image-based HTP can be used to bridge the phenotype–genotype gap for yield prediction, root phenotyping, climate-resilient crop development, pathogen and pest detection, and quantitative trait measurement for long-term food security. Finally, we will discuss some conceptual issues and provide suggestions for bridging the phenotype–genotype divide. There is little question that precise HTP will speed up plant genetic advancements and help to usher in the next crop breeding revolution.

The morphological traits of wheat grain strongly influence on yield and directly affect the grain yield of the crop. The necessity to overcome the human demand of wheat the grain yield should be intensified. The current experiment was organized to study the morphological traits of wheat and their association with yield. The experiment was done in the randomized complete block design including three replications and twenty genotypes under normal condition in cropping season of 2021. The result of analysis of variance indicates that there is highly significant difference among the studied genotypes, traits like spikelet per spike (SPS), flag leaf area(FLA), grain yield per spike(GYS), number of grains per spike(GPS), biological yield (BY) and grain yield per plant(GYP) showed the genetic potential and variability among them. While traits plant height (PH) and peduncle length (PL) are significant. Correlation analysis showed that grain yield per plant is highly associated with flag leaf area (0.78**) followed by biological yield which is highly correlated with plant height (0.77**) and number of grain per spike was also highly correlated with spikelet per spike (0.70**).While spikelet per spike and number of grains per spike correlated non-significantly with plant height (0.21ns), (0.23ns) and biological yield correalted non-significantly with spikelet per spike (0.21ns).The highest mean values recorded by the genotype G3 for the traits SPS (21.22), PL (16.74) and BY (23.33), followed by the genotype G14 for the traits SPS (23.22), PL (17.36), FLA (15), GPS (35.83) and by the genotype G19 for the traits PH (94.63), BY (22.23), GPS (33.16). Hence, in breeding or selection program, to develop the high yield of wheat cultivars in selection or breeding program, these yield related traits should have strong and positive association.

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.

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.