Transcriptomics for Drought Stress Mediated by Biological Processes in-relation to Key Regulated Pathways in Gossypium darwinii.

BACKGROUND: Wild cotton Gossypium darwinii, an allotetraploid harbours important traits useful for tolerating abiotic stress, i.e., drought, salt and good genetic stability, hence these characteristics can be transferred to cultivated cotton for genetic improvement. MATERIALS AND METHODS: In this study, we analyzed the RNA-seq transcriptomes from leaves of G. darwinii seedlings with and without drought stress. A total of 86.7 million valid reads with an average length of 95.79 bp were generated from the two samples and 58,960 transcripts with a length of more than 500 bp were assembled. We searched the known proteins on the strength of sequence similarity; these transcripts were annotated with COG, KEGG and GO functional categories. According to gene expression abundance RPKM value, we carried out RT-qPCR analysis to determine the expression pattern of the obtained transcription factors. RESULTS: A total of 58,960 genes was differentially expressed (DEG), with 32,693 and 25,919 genes found to be upregulated and downregulated, respectively. Through gene ontology and KEGG pathways, the upregulated genes were found to associate with all the GO terms, molecular functions (MF), biological process (BP) and cellular components (CC), which are highly linked to enhancing drought stress tolerance. CONCLUSION: The study provides an in-depth knowledge of regulation of pathways and genes involved in photosynthesis during drought stress in G. darwinii. These pathways and genes were found to be significantly downregulated and this information could be further utilized by cotton breeders in developing a more drought tolerant cotton germplasm.

Estimating genetic variability among diverse lentil collections through novel multivariate techniques.

Lentil is an important food legume throughout the world and Pakistan stands at 18th position with 8,610 tons production from 17,457 hectares. It is rich in protein, carbohydrates, fat, fiber, and minerals that can potentially meet food security and malnutrition issues, particularly in South Asia. Two hundred and twenty lentil genotypes representing Pakistan (178), Syria (14), and the USA (22) including 6 from unknown origins were studied for yield, yield contributing traits, and cooking time (CT). Genotype 6122 (Pakistan) performed the best during both years with seed yield per plant (SY) 68±1.7 g, biological yield per plant (BY) 264±2.8 g, pod size (PS) 0.61±0.01 cm, number of seeds per pod (NSP) 2, cooking time (CT) 11 minutes, with no hard seed (HS). The genotypes 6122 (Pakistan) and 6042 (Syria) produced the highest BY, hence these have the potential to be an efficient source of fodder, particularly during extreme winter months. The genotypes 5698 (Pakistan) and 6015 (USA) were late in maturity during 2018-19 while 24783 and 5561 matured early in 2019. A minimum CT of 10 minutes was taken by the genotypes 6074 and 5745 of Pakistani origin. The lowest CT saves energy, time, and resources, keeps flavor, texture, and improves protein digestibility, hence the genotypes with minimum CT are recommended for developing better lentil cultivars. Pearson correlation matrix revealed significant association among several traits, especially SY with BY, PS, and NSP which suggests their use for the future crop improvement program. The PCA revealed a considerable reduction in components for the selection of suitable genotypes with desired traits that could be utilized for future lentil breeding. Structural Equational Model (SEM) for SY based on covariance studies indicated the perfect relationship among variables. Further, hierarchical cluster analysis establishes four clusters for 2017-18, whereas seven clusters for 2018-19. Cluster 4 of 2017-18 and cluster 5 of 2018-19 exhibited the genotypes with the best performance for most of the traits (SY, BY, PS, NSP, CT, and HS). Based on heritability; HSW, SY, BY, NSP were highly heritable, hence these traits are expected for selecting genotypes with genes of interest and for future lentil cultivars. In conclusion, 10 genotypes (5664, 5687, 6084, 6062, 6122, 6058, 6087, 5689, 6042 and 6074) have been suggested to evaluate under multi-location environments for selection of the best one/s or could be utilized in hybridization in future lentil breeding programs.

Characterization of the genetic basis of local adaptation of wheat landraces from Iran and Pakistan using genome-wide association study.

Characterization of genomic regions underlying adaptation of landraces can reveal a quantitative genetics framework for local wheat (Triticum aestivum L.) adaptability. A collection of 512 wheat landraces from the eastern edge of the Fertile Crescent in Iran and Pakistan were genotyped using genome-wide single nucleotide polymorphism markers generated by genotyping-by-sequencing. The minor allele frequency (MAF) and the heterozygosity (H) of Pakistani wheat landraces (MAF = 0.19, H = 0.008) were slightly higher than the Iranian wheat landraces (MAF = 0.17, H = 0.005), indicating that Pakistani landraces were slightly more genetically diverse. Population structure analysis clearly separated the Pakistani landraces from Iranian landraces, which indicates two separate adaptability trajectories. The large-scale agro-climatic data of seven variables were quite dissimilar between Iran and Pakistan as revealed by the correlation coefficients. Genome-wide association study identified 91 and 58 loci using agroclimatic data, which likely underpin local adaptability of the wheat landraces from Iran and Pakistan, respectively. Selective sweep analysis identified significant hits on chromosomes 4A, 4B, 6B, 7B, 2D, and 6D, which were colocalized with the loci associated with local adaptability and with some known genes related to flowering time and grain size. This study provides insight into the genetic diversity with emphasis on the genetic architecture of loci involved in adaptation to local environments, which has breeding implications.

Genome-wide variation patterns between landraces and cultivars uncover divergent selection during modern wheat breeding.

KEY MESSAGE: Genetic diversity, population structure, LD decay, and selective sweeps in 687 wheat accessions were analyzed, providing relevant guidelines to facilitate the use of the germplasm in wheat breeding. Common wheat (Triticum aestivum L.) is one of the most widely grown crops in the world. Landraces were subjected to strong human-mediated selection in developing high-yielding, good quality, and widely adapted cultivars. To investigate the genome-wide patterns of allelic variation, population structure and patterns of selective sweeps during modern wheat breeding, we tested 687 wheat accessions, including landraces (148) and cultivars (539) mainly from China and Pakistan in a wheat 90 K single nucleotide polymorphism array. Population structure analysis revealed that cultivars and landraces from China and Pakistan comprised three relatively independent genetic clusters. Cultivars displayed lower nucleotide diversity and a wider average LD decay across whole genome, indicating allelic erosion and a diversity bottleneck due to the modern breeding. Analysis of genetic differentiation between landraces and cultivars from China and Pakistan identified allelic variants subjected to selection during modern breeding. In total, 477 unique genome regions showed signatures of selection, where 109 were identified in both China and Pakistan germplasm. The majority of genomic regions were located in the B genome (225), followed by the A genome (175), and only 77 regions were located in the D genome. EigenGWAS was further used to identify key selection loci in modern wheat cultivars from China and Pakistan by comparing with global winter wheat and spring wheat diversity panels, respectively. A few known functional genes or loci found within these genome regions corresponded to known phenotypes for disease resistance, vernalization, quality, adaptability and yield-related traits. This study uncovered molecular footprints of modern wheat breeding and explained the genetic basis of polygenic adaptation in wheat. The results will be useful for understanding targets of modern wheat breeding, and in devising future breeding strategies to target beneficial alleles currently not pursued.