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.

Small-Sized Nanophosphorus Has a Positive Impact on the Performance of Fenugreek Plants under Soil-Water Deficit Stress: A Case Study under Field Conditions

Phosphorus (P) is an essential macronutrient necessary for plant growth, development, and reproduction. Two field experiments were carried out in 2018/2019 and 2019/2020 on P-deficient soil to evaluate the impact of foliar fertilization with nanophosphorus (nP) on growth, yield, and physio-biochemical indices, as well as trigonelline content of fenugreek plants under deficient irrigation (dI) stress (a deficit of 20 and 40% of crop evapotranspiration; dI-20 and dI-40). The growth and yield traits, leaf integrity (relative water content and membrane stability index), photosynthetic pigment contents, leaf and seed P contents, and stem and leaf anatomical features significantly decreased under dI-20, with greater reductions recorded under dI-40. In contrast, water-use efficiency, osmoprotective compounds, including free amino acids, soluble sugars, proline, and trigonelline, along with antioxidant contents (ascorbate, glutathione, phenolics, and flavonoids) and their activity increased significantly under both dI-20 and dI-40. However, foliar feeding with nano-P considerably increased plant growth and yield traits, leaf integrity, photosynthetic pigments contents, leaf and seed P contents, and anatomical features. Besides, water-use efficiency, osmoprotectant contents, and antioxidant content and activity were further increased under both dI-20 and dI-40. The positive effects were more pronounced with the smaller nP (25 nm) than the larger nP (50 nm). The results of this study backed up the idea of using foliar nourishment with nP, which can be effective in modulating fenugreek plant growth and seed production.

Identification of Candidate Forage Yield Genes in Sorghum (Sorghum bicolor L.) Using Integrated Genome-Wide Association Studies and RNA-Seq

Genetic dissection of forage yield traits is critical to the development of sorghum as a forage crop. In the present study, association mapping was performed with 85,585 SNP markers on four forage yield traits, namely plant height (PH), tiller number (TN), stem diameter (SD), and fresh weight per plant (FW) among 245 sorghum accessions evaluated in four environments. A total of 338 SNPs or quantitative trait nucleotides (QTNs) were associated with the four traits, and 21 of these QTNs were detected in at least two environments, including four QTNs for PH, ten for TN, six for SD, and one for FW. To identify candidate genes, dynamic transcriptome expression profiling was performed at four stages of sorghum development. One hundred and six differentially expressed genes (DEGs) that were enriched in hormone signal transduction pathways were found in all stages. Weighted gene correlation network analysis for PH and SD indicated that eight modules were significantly correlated with PH and that three modules were significantly correlated with SD. The blue module had the highest positive correlation with PH and SD, and the turquoise module had the highest negative correlation with PH and SD. Eight candidate genes were identified through the integration of genome-wide association studies (GWAS) and RNA sequencing. Sobic.004G143900, an indole-3-glycerol phosphate synthase gene that is involved in indoleacetic acid biosynthesis, was down-regulated as sorghum plants grew in height and was identified in the blue module, and Sobic.003G375100, an SD candidate gene, encoded a DNA repair RAD52-like protein 1 that plays a critical role in DNA repair-linked cell cycle progression. These findings demonstrate that the integrative analysis of omics data is a promising approach to identify candidate genes for complex traits.

Genetic parameters controlling the inheritance of glaucousness and yield traits in bread wheat

Wheat breeders frequently use generation mean analysis to obtain information on the type of gene action involved in inheriting a trait to choose the helpful breeding procedure for trait improvement. The present study was carried out to study the inter-allelic and intra-allelic gene action and inheritance of glaucousness, earliness and yield traits in a bread wheat cross between divergent parents in glaucousness and yield traits; namely Mut-2 (P1) and Sakha 93 (P2). The experimental material included six populations, i.e. P1, P2, F1, F2, BC1, and BC2 for this wheat cross. A randomized complete block design with three replications was used, and a six parameters model was applied. Additive effects were generally more critical than dominance for all studied traits, except for plant height (PH) and grain yield/plant (GYPP). The duplicate epistasis was observed in spike length; SL, spikes/plant; SPP and days to heading; DTH. All six types of allelic and non-allelic interaction effects controlled SL, GYPP, DTH and glaucousness. All three types of epistasis, i.e. additive x additive, additive x dominance, and dominance x dominance, are essential in determining the inheritance of four traits (SL, GYPP, DTH and glaucousness). Dominance × dominance effects were higher in magnitude than additive × dominance and additive × additive in most traits. The average degree of dominance was minor than unity in six traits (glaucousness, grains/spike, spike weight, days to maturity, 100-grain weight and SL), indicating partial dominance and selection for these traits might be more effective in early generations. Meanwhile, the remaining traits (PH, SPP, GYPP and DTH) had a degree of dominance more than unity, indicating that overdominance gene effects control such traits and it is preferable to postpone selection to later generations. The highest values of narrow-sense heritability and genetic advance were recorded by glaucousness trait followed by SL and SPP, indicating that selection in segregating generations would be more effective than other traits.

Comparative study on the phenology, gender and yield components of cucumber (Cucumis sativus L.) varieties

The intensity of sex expression is important in crops, including cucumber, since sex form and flowering have direct effects on date of harvesting and yield. Two groups of cucumber comprising a native variety (Odukpani) and elite varieties (Griffaton, Poinsett, Ashley, Marketmore and Monarch) were evaluated in 2015 and 2016 cropping seasons at the Teaching and Research Farm, College of Agriculture, Garkawa, Plateau State; to assess flowering, sex expression and some yield traits. The experimental design was randomized complete block design with the 6 cucumber varieties as the treatments, replicated five times. The two groups differed significantly (p < 0.05) in phonological, flowering and yield traits assessed. The elite varieties were superior with respect to flowering traits, as they flowered early. The intra-population hierarchical cluster analysis of quantitative traits grouped the elite varieties in one main cluster and the native variety (Odukpani) alienated as an outlier. The cluster plots showed that Odukpani was robust in vegetative growth, produced few but larger fruit size and flowering was delayed for over two weeks. Conversely, the elite varieties flowered early, produced more flowers and recorded superior number of fruits per plant. The profuse production of pistillate flowers by the elite varieties had pronounced yield advantage over the local variety. Hybridization between the two groups of cucumber would make a mark in the drive for sustainable cucumber fruit yield.

Heterosis and combining ability studies by Line × tester analysis for fruit biochemical, morpho-physiological, and yield traits governing shelf life in tomato (Solanum lycopersicum L.)

Improving tomatoes keeping quality is crucial for reducing post-harvest losses. Knowledge on heterosis, and combining ability is pre requisite for breeding high yielding and good shelf life heterotic hybrids. An investigation was undertaken with each of 3 lines, testers, and 9 hybrids to identify desirable parents and crosses for 20 fruit biochemical, morpho-physiological, and yield traits and to elucidate nature of gene action for shelf life and its contributing traits through Line × Tester analysis. The lines contributed to most of hybrids variability than testers and fruit quality traits had higher degree of SCA variance as compared to GCA variance. pH, ascorbic acid, fruit firmness, and plant height governed by additive gene action. Lycopene, titratable acidity, TSS, calcium, magnesium, pericarp thickness, pulp content, locule number, fruit length, diameter, weight, shelf life, number of branches, number of clusters, number of fruit/cluster, and yield/plant were under the control of non-additive gene action. All the lines and Arka Saurabh were best general combiners and IIHR 2349 × Arka Vikas, IIHR 2349 × Arka Saurabh, IIHR 2358 × Arka Ahuti and IIHR 2357 × Arka Ahuti were the best specific combiner in producing heterotic hybrids. IIHR 2349 × Arka Vikas and IIHR 2349 × Arka Saurabh were promising hybrids for high yield and shelf life. The crosses involved both parents with high, one parent with high and other with low and both parents with low good overall general combining ability status respectively indicated the additive, non-additive and epistatic gene action in fruit quality and yield traits inheritance.