Beneficial Alleles Research Articles

A numerical framework for genetic hitchhiking in populations of variable size.

Natural selection on beneficial or deleterious alleles results in an increase or decrease, respectively, of their frequency within the population. Due to chromosomal linkage, the dynamics of the selected site affect the genetic variation at nearby neutral loci in a process commonly referred to as genetic hitchhiking. Changes in population size, however, can yield patterns in genomic data that mimic the effects of selection. Accurately modeling these dynamics is thus crucial to understanding how selection and past population size changes impact observed patterns of genetic variation. Here, we model the evolution of haplotype frequencies with the Wright-Fisher diffusion to study the impact of selection on linked neutral variation. Explicit solutions are not known for the dynamics of this diffusion when selection and recombination act simultaneously. Thus, we present a method for numerically evaluating the Wright-Fisher diffusion dynamics of 2 linked loci separated by a certain recombination distance when selection is acting. We can account for arbitrary population size histories explicitly using this approach. A key step in the method is to express the moments of the associated transition density, or sampling probabilities, as solutions to ordinary differential equations. Numerically solving these differential equations relies on a novel accurate and numerically efficient technique to estimate higher order moments from lower order moments. We demonstrate how this numerical framework can be used to quantify the reduction and recovery of genetic diversity around a selected locus over time and elucidate distortions in the site-frequency-spectra of neutral variation linked to loci under selection in various demographic settings. The method can be readily extended to more general modes of selection and applied in likelihood frameworks to detect loci under selection and infer the strength of the selective pressure.

GgComp enables dissection of germplasm resources and construction of a multiscale germplasm network in wheat.

Accurate germplasm characterization is a vital step for accelerating crop genetic improvement, which remains largely infeasible for crops such as bread wheat (Triticum aestivum L.), which has a complex genome that undergoes frequent introgression and contains many structural variations. Here, we propose a genomic strategy called ggComp, which integrates resequencing data with copy number variations and stratified single-nucleotide polymorphism densities to enable unsupervised identification of pairwise germplasm resource-based Identity-By-Descent (gIBD) blocks. The reliability of ggComp was verified in wheat cultivar Nongda5181 by dissecting parental-descent patterns represented by inherited genomic blocks. With gIBD blocks identified among 212 wheat accessions, we constructed a multi-scale genomic-based germplasm network. At the whole-genome level, the network helps to clarify pedigree relationship, demonstrate genetic flow, and identify key founder lines. At the chromosome level, we were able to trace the utilization of 1RS introgression in modern wheat breeding by hitchhiked segments. At the single block scale, the dissected germplasm-based haplotypes nicely matched with previously identified alleles of “Green Revolution” genes and can guide allele mining and dissect the trajectory of beneficial alleles in wheat breeding. Our work presents a model-based framework for precisely evaluating germplasm resources with genomic data. A database, WheatCompDB (http://wheat.cau.edu.cn/WheatCompDB/), is available for researchers to exploit the identified gIBDs with a multi-scale network.

One-step base editing in multiple genes by direct embryo injection for pig trait improvement.

The precise and simultaneous acquisition of multiple beneficial alleles in the genome is in great demand for the development of elite pig breeders. Cytidine base editors (CBEs) that convert C:G to T:A have emerged as powerful tools for single-nucleotide replacement. Whether CBEs can effectively mediate C-to-T substitution at multiple sites/loci for trait improvement by direct zygote injection has not been verified in large animals. Here, we determined the editing efficiency of four CBE variants in porcine embryonic fibroblast cells and embryos. The findings showed that hA3A-BE3-Y130F and hA3A-eBE-Y130F consistently resulted in increased base-editing efficiency and low toxic effects in embryonic development. Further, we verified that using a one-step approach, direct zygote microinjection of the CBE system can generate pigs harboring multiple point mutations. Our process resulted in a stop codon in CD163 and myostatin (MSTN) and introduced a beneficial allele in insulin-like growth factor-2 (IGF2). The pigs showed disrupted expression of CD163 and MSTN and increased expression of IGF2, which significantly improved growth performance and infectious disease resistance. Our approach allows immediate introduction of multiple mutations in transgene-free animals to comprehensively improve economic traits through direct embryo microinjection, providing a potential new route to produce elite pig breeders.

Resequencing worldwide spinach germplasm for identification of field resistance QTLs to downy mildew and assessment of genomic selection methods.

Downy mildew, commercially the most important disease of spinach, is caused by the obligate oomycete Peronospora effusa. In the past two decades, new pathogen races have repeatedly overcome the resistance used in newly released cultivars, urging the need for more durable resistance. Commercial spinach cultivars are bred with major R genes to impart resistance to downy mildew pathogens and are effective against some pathogen races/isolates. This work aimed to evaluate the worldwide USDA spinach germplasm collections and commercial cultivars for resistance to downy mildew pathogen in the field condition under natural inoculum pressure and conduct genome wide association analysis (GWAS) to identify resistance-associated genomic regions (alleles). Another objective was to evaluate the prediction accuracy (PA) using several genomic prediction (GP) methods to assess the potential implementation of genomic selection (GS) to improve spinach breeding for resistance to downy mildew pathogen. More than four hundred diverse spinach genotypes comprising USDA germplasm accessions and commercial cultivars were evaluated for resistance to downy mildew pathogen between 2017-2019 in Salinas Valley, California and Yuma, Arizona. GWAS was performed using single nucleotide polymorphism (SNP) markers identified via whole genome resequencing (WGR) in GAPIT and TASSEL programs; detected 14, 12, 5, and 10 significantly associated SNP markers with the resistance from four tested environments, respectively; and the QTL alleles were detected at the previously reported region of chromosome 3 in three of the four experiments. In parallel, PA was assessed using six GP models and seven unique marker datasets for field resistance to downy mildew pathogen across four tested environments. The results suggest the suitability of GS to improve field resistance to downy mildew pathogen. The QTL, SNP markers, and PA estimates provide new information in spinach breeding to select resistant plants and breeding lines through marker-assisted selection (MAS) and GS, eventually helping to accumulate beneficial alleles for durable disease resistance.

Haldane\u2019s formula in Cannings models: the case of moderately strong selection

For a class of Cannings models we prove Haldane’s formula, pi (s_N) sim frac{2s_N}{rho ^2}, for the fixation probability of a single beneficial mutant in the limit of large population size N and in the regime of moderately strong selection, i.e. for s_N sim N^{-b} and 0< b<1/2. Here, s_N is the selective advantage of an individual carrying the beneficial type, and rho ^2 is the (asymptotic) offspring variance. Our assumptions on the reproduction mechanism allow for a coupling of the beneficial allele’s frequency process with slightly supercritical Galton–Watson processes in the early phase of fixation.

Natural Variation in OsMKK3 Contributes to Grain Size and Chalkiness in Rice.

Rice (Oryza sativa L.) is an important staple food crop for more than half of the world’s population. Enhancing the grain quality and yield of rice to meet growing demand remains a major challenge. Here, we show that OsMKK3 encode a MAP kinase kinase that controls grain size and chalkiness by affecting cell proliferation in spikelet hulls. We showed that OsSPL16, GS5, and GIF1 have a substantial effect on the OsMKK3-regulated grain size pathway. OsMKK3 has experienced strong directional selection in indica and japonica. Wild rice accessions contained four OsMKK3 haplotypes, suggesting that the OsMKK3 haplotypes present in cultivated rice likely originated from different wild rice accessions during rice domestication. OsMKK3-Hap1, gs3, and gw8 were polymerized to enhance the grain length. Polymerization of beneficial alleles, such as OsMKK3-Hap1, gs3, gw8, fgr, alk, chalk5, and wx, also improved the quality of hybrid rice. Overall, the results indicated that beneficial OsMKK3 alleles could be used for genomic-assisted breeding for rice cultivar improvement and be polymerized with other beneficial alleles.

Heritability and Genetic Advance as Genetic Indicators for Improvement in Two Cotton Crosses

The primary breeding goal for the Egyptian cotton breeding program is how to genetically improve both yield and fibre quality traits, while most of these agronomically traits are biometric traits. The objective of the present study is to evaluate variability and estimate frequency of transgressive segregants in order to isolate early superior individual plants which exceeding the better parent for some yield and fiber quality traits in two intraspecific cotton crosses in early transgressive segregating generation (F2 ). The F1 was highly significant superior than the better parent (Giza 97 and Giza 94) of the two crosses for all the studied traits except boll weight and lint %. Most of the studied traits in F2 generation showed high values of broad sense heritability coupled with low GAM % indicated that these traits controlled by non-additive gene action. All the studied traits had positive skewness sign except for lint %. Presley index and uniformity index for the two cotton crosses and upper half mean for cross II showed negative skewness. The negative skewness indicated that the population had more plants frequency with higher mean values than population mean and controlled by dominancy alleles. While, the traits that had positive skewness are controlled by additive gene action. The two cotton crosses showed transgressive segregants for all the studied traits. Cross I has higher transgressive index for yield traits than cross II, while cross II has the same trend for fiber quality traits than cross I. These results indicated that the both parents of the two cotton crosses had different alleles and genes governing the respective studied traits, which will help cotton breeder to combine beneficial alleles into a single genotype by rigorous selection process. This strategy could be used to improve many economic biometric traits by using better and stringent selection procedure to enhance Egyptian cotton productivity which is major concern in Egypt. The breeder can use transgressive segregation as an indicator of genetic variability to select the most superior plants.

The classical hitchhiking model with continuous mutational pressure and purifying selection.

Detecting selective sweeps driven by strong positive selection and localizing the targets of selection in the genome play a major role in modern population genetics and genomics. Most of these analyses are based on the classical model of genetic hitchhiking proposed by Maynard Smith and Haigh (1974, Genetical Research, 23, 23). Here, we consider extensions of the classical two‐locus model. Introducing mutation at the strongly selected site, we analyze the conditions under which soft sweeps may arise. We identify a new parameter (the ratio of the beneficial mutation rate to the selection coefficient) that characterizes the occurrence of multiple‐origin soft sweeps. Furthermore, we quantify the hitchhiking effect when the polymorphism at the linked locus is not neutral but maintained in a mutation‐selection balance. In this case, we find a smaller relative reduction of heterozygosity at the linked site than for a neutral polymorphism. In our analysis, we use a semi‐deterministic approach; i.e., we analyze the frequency process of the beneficial allele in an infinitely large population when its frequency is above a certain threshold; however, for very small frequencies in the initial phase after the onset of selection we rely on diffusion theory.

Analysis of Chromosome Associations during Early Meiosis in Wheat Lines Carrying Chromosome Introgressions from Agropyron cristatum.

Crested wheatgrass (Agropyron cristatum L. Gaertn., genome P), included in the Triticeae tribe (family Poaceae), is one of the most important grasses in temperate regions. It has been valued as a donor of important agronomic traits for wheat improvement, including tolerance to cold, drought, and high salinity, as well as resistance to leaf rust, stripe rust, and powdery mildew. For successful incorporation of beneficial alleles into wheat, it is essential that recombination between wheat and A. cristatum chromosomes occurs. In this work, we analysed chromosome associations during meiosis in wheat lines carrying chromosome introgressions from A. cristatum chromosomes 5P and 6P in the presence and absence of Ph1 locus using fluorescence in situ hybridisation. The results showed that the Ph1 locus does not affect chromosome associations between A. cristatum and wheat chromosomes because there were no interspecific chromosome associations; therefore, no recombination between chromosomes from wheat and Agropyron were observed in the absence of the Ph1 locus. The 5P and 6P A. cristatum chromosomes do not have a suppressor effect on the Ph1 locus. Wheat univalents in metaphase I suggest that Agropyron chromosomes might carry genes having a role in wheat homologous chromosome associations. Putative effect of the Agropyron genes on wheat chromosome associations does not interact with the Ph1 locus.

Association mapping of drought tolerance and agronomic traits in rice (Oryza sativa L.) landraces

BackgroundAsian cultivars were predominantly represented in global rice panel selected for sequencing and to identify novel alleles for drought tolerance. Diverse genetic resources adapted to Indian subcontinent were not represented much in spite harboring useful alleles that could improve agronomic traits, stress resilience and productivity. These rice accessions are valuable genetic resource in developing rice varieties suited to different rice ecosystem that experiences varying drought stress level, and at different crop stages. A core collection of rice germplasm adapted to Southwestern Indian peninsular genotyped using SSR markers and characterized by contrasting water regimes to associate genomic regions for physiological, root traits and yield related traits. Genotyping-By-Sequencing of selected accessions within the diverse panel revealed haplotype variation in genic content within genomic regions mapped for physiological, morphological and root traits.ResultsDiverse rice panel (99 accessions) were evaluated in field and measurements on plant physiological, root traits and yield related traits were made over five different seasons experiencing varying drought stress intensity at different crop stages. Traits like chlorophyll stability index, leaf rolling, days to 50% flowering, chlorophyll content, root volume and root biomass were identified as best predictors of grain yield under stress. Association mapping revealed genetic variation among accessions and revealed 14 genomic targets associated with different physiological, root and plant production traits. Certain accessions were found to have beneficial allele to improve traits, plant height, root length and spikelet fertility, that contribute to the grain yield under stress. Genomic characterization of eleven accessions revealed haplotype variation within key genomic targets on chromosomes 1, 4, 6 and 11 for potential use as molecular markers to combine drought avoidance and tolerance traits. Genes mined within the genomic QTL intervals identified were prioritized based on tissue specific expression level in publicly available rice transcriptome data.ConclusionThe genetic and genomic resources identified will enable combining traits with agronomic value to optimize yield under stress and hasten trait introgression into elite cultivars. Alleles associated with plant height, specific leaf area, root length from PTB8 and spikelet fertility and grain weight from PTB26 can be harnessed in future rice breeding program.

Metabolomics for Crop Breeding: General Considerations.

The development of new, more productive varieties of agricultural crops is becoming an increasingly difficult task. Modern approaches for the identification of beneficial alleles and their use in elite cultivars, such as quantitative trait loci (QTL) mapping and marker-assisted selection (MAS), are effective but insufficient for keeping pace with the improvement of wheat or other crops. Metabolomics is a powerful but underutilized approach that can assist crop breeding. In this review, basic methodological information is summarized, and the current strategies of applications of metabolomics related to crop breeding are explored using recent examples. We briefly describe classes of plant metabolites, cellular localization of metabolic pathways, and the strengths and weaknesses of the main metabolomics technique. Among the commercialized genetically modified crops, about 50 with altered metabolic enzyme activities have been identified in the International Service for the Acquisition of Agri-biotech Applications (ISAAA) database. These plants are reviewed as encouraging examples of the application of knowledge of biochemical pathways. Based on the recent examples of metabolomic studies, we discuss the performance of metabolic markers, the integration of metabolic and genomic data in metabolic QTLs (mQTLs) and metabolic genome-wide association studies (mGWAS). The elucidation of metabolic pathways and involved genes will help in crop breeding and the introgression of alleles of wild relatives in a more targeted manner.

New drought‐adaptive loci underlying candidate genes on wheat chromosome 4B with improved photosynthesis and yield responses

Flag leaf serves as an essential source of assimilates during grain filling, thereby contributing to grain yield up to 48%. Thus, high-throughput phenotyping of flag leaves is crucial to determine their physiological and genetic basis of yield formation and drought adaptation. Here, we utilized 200 wheat cultivars to identify drought-adaptive loci underlying candidate genes associated with flag leaf biomass and photosynthesis-related traits using a genome-wide association study (GWAS). GWAS revealed 21 significant marker-trait associations for key photosynthetic traits in response to drought stress. Analysis of linkage disequilibrium (LD) in these SNPs intervals discovered 103 significant SNPs that established distinct LD blocks containing a total of 382 candidate genes putatively involved in physiological processes, including photosynthesis and water responses. Further, in silico transcript analysis identified two candidate genes in locus AX-580365925 on chromosome 4B, those were found to be highly expressed under drought and associated with proton-transporting ATP synthase activity and stress response pathways. Accordingly, we identified significant allelic haplotype differences on this same locus. The tolerant haplotype (higher chlorophyll content under drought) representing major allele was more abundant and stably increased photosynthetic efficiency and yield under drought scenarios. Collectively, this study offers new adaptive loci and beneficial alleles to reshape the flag leaf physiological and associated photosynthetic components for better yield and sustainability to water-deficit stress.

Introducing Beneficial Alleles from Plant Genetic Resources into the Wheat Germplasm.

Simple SummaryMany crops including wheat have a narrow genetic base after hundreds of years of breeding and selection. This makes it difficult to breed new varieties with increased yields to feed the growing global population, and with stronger tolerance to the wider range of biotic and abiotic stresses that are anticipated with climate change. Thus, there is a need to introduce new genetic diversity into wheat breeding programs. Plant genetic resources stored in genebanks and the wild relatives of crops are potential sources of new genetic diversity. Here, we discuss the importance of these resources for breeding new wheat cultivars, and outline where they are currently stored and used. We also discuss pre-breeding, where genetic regions associated with desirable traits are identified and transferred into materials ready for use in breeding programs. Pre-breeding in wheat, when conducted in close collaboration with breeders, farmers, and end-users, has contributed to many outstanding varieties and novel beneficial diversity. This review addresses various genetic and genomic considerations for the strategic transfer of this useful diversity.Wheat (Triticum sp.) is one of the world’s most important crops, and constantly increasing its productivity is crucial to the livelihoods of millions of people. However, more than a century of intensive breeding and selection processes have eroded genetic diversity in the elite genepool, making new genetic gains difficult. Therefore, the need to introduce novel genetic diversity into modern wheat has become increasingly important. This review provides an overview of the plant genetic resources (PGR) available for wheat. We describe the most important taxonomic and phylogenetic relationships of these PGR to guide their use in wheat breeding. In addition, we present the status of the use of some of these resources in wheat breeding programs. We propose several introgression schemes that allow the transfer of qualitative and quantitative alleles from PGR into elite germplasm. With this in mind, we propose the use of a stage-gate approach to align the pre-breeding with main breeding programs to meet the needs of breeders, farmers, and end-users. Overall, this review provides a clear starting point to guide the introgression of useful alleles over the next decade.

Assimilate highway to sink organs – Physiological consequences of SP6A overexpression in transgenic potato (Solanum tuberosum L.)

Leaf/stem-specific overexpression of SP6A, the FLOWERING LOCUS T homolog in potato (Solanum tuberosum), was previously shown to induce tuberization leading to higher tuber numbers and yield under ambient and abiotic stress conditions. In this study, we investigated the mechanism underlying SP6A action. Overexpression of SP6A reduced shoot growth, mainly by inhibition of stem elongation and secondary growth, and by repression of apical bud outgrowth. In contrast, root growth and lateral shoot emergence from basal nodes was promoted. Tracer experiments using the fluorescent sucrose analogue esculin revealed that stems of SP6A overexpressing plants transport assimilates more efficiently to belowground sinks, e.g. roots and tubers, compared to wild-type plants. This was accompanied by a lower level of sucrose leakage from the transport phloem into neighboring parenchyma cells and the inhibition of flower formation. We demonstrate the ability of SP6A to control assimilate allocation to belowground sinks and postulate that selection of beneficial SP6A alleles will enable potato breeding to alter plant architecture and to increase tuber yield under conditions of expected climate change.

Evolution of resistance under alternative models of selective interference.

The use of multiple pesticides or drugs can lead to a simultaneous selection pressure for resistance alleles at different loci. Models of resistance evolution focus on how this can delay the spread of resistance through a population, but often neglect how this can also reduce the probability that a resistance allele spreads. This neglected factor has been studied in a parallel literature as selective interference. Models of interference use alternative constructions of fitness, where selection coefficients from different loci either add or multiply. Although these are equivalent under weak selection, the two constructions make alternative predictions under the strong selection that characterizes resistance evolution. Here, simulations are used to examine the effects of interference on the probability of fixation and time to fixation of a new and strongly beneficial mutation in the presence of another strongly beneficial allele with variable starting frequency. The results from simulations show a complicated pattern of effects. The key result is that, under multiplicativity, the presence of the strongly beneficial allele leads to a small reduction in the probability of fixation for the new beneficial mutation up to ~10%, and a negligible increase in the average time to fixation up to ~2%, whereas under additivity, the effect is more substantial at up to ~50% for the probability of fixation and ~100% for the average time to fixation. Consequently, the effect of interference is only an important feature of resistance evolution under additivity. Current evidence from studies of experimental evolution provides widespread support for the basic features of additivity, which suggests that interference may afford resistance a different pattern of evolution than other adaptations: rather than the gradual and simultaneous selection of many alleles with small effects, the rapid evolution of resistance may involve the sequential selection of alleles with large effects.

Registration of three peanut allotetraploid interspecific hybrids resistant to late leaf spot disease and tomato spotted wilt

AbstractCultivated peanut (Arachis hypogaea L.) has a narrow genetic base and is isolated from its wild relatives. This genetic bottleneck results in a lack of strong resistance to biotic and abiotic stress. However, high levels of genetic variation and resistance exist among the wild relatives. In order to enlarge the genetic base of cultivated peanut and introgress beneficial alleles from the wild relatives, interspecific hybrids were produced among a set of selected diploid species. Upon colchicine treatment, fertile allotetraploids were recovered from three combinations including (A. ipaënsis KG 30076 × A. correntina GKP 9530)4x (Reg. no. GP‐241, PI 695391), (A. ipaënsis KG 30076 × A. duranensis KGBSPSc 30060)4x (Reg. no. GP‐242, PI 695392), and (A. valida KG30011 × A. stenosperma V 10309)4x (Reg. no. GP‐243, PI 695393). All of them demonstrated high levels of resistance to leaf spot diseases in the field. Tolerance to Tomato spotted wilt virus was found in (A. valida KG 30011 × A. stenosperma V 10309)4x. These newly created allotetraploids are cross‐compatible with cultivated peanut. These genetic resources will provide peanut breeding researchers with new sources of disease resistances to improve the agronomic performance of cultivated peanut.

Recombination Facilitates Adaptive Evolution in Rhizobial Soil Bacteria.

Homologous recombination is expected to increase natural selection efficacy by decoupling the fate of beneficial and deleterious mutations and by readily creating new combinations of beneficial alleles. Here, we investigate how the proportion of amino acid substitutions fixed by adaptive evolution () depends on the recombination rate in bacteria. We analyze 3,086 core protein-coding sequences from 196 genomes belonging to five closely related species of the genus Rhizobium. These genes are found in all species and do not display any signs of introgression between species. We estimate using the site frequency spectrum (SFS) and divergence data for all pairs of species. We evaluate the impact of recombination within each species by dividing genes into three equally sized recombination classes based on their average level of intragenic linkage disequilibrium. We find that varies from 0.07 to 0.39 across species and is positively correlated with the level of recombination. This is both due to a higher estimated rate of adaptive evolution and a lower estimated rate of nonadaptive evolution, suggesting that recombination both increases the fixation probability of advantageous variants and decreases the probability of fixation of deleterious variants. Our results demonstrate that homologous recombination facilitates adaptive evolution measured by in the core genome of prokaryote species in agreement with studies in eukaryotes.

SNP-based assessment of genetic purity and diversity in maize hybrid breeding.

Assessment of genetic purity of parental inbred lines and their resultant F1 hybrids is an essential quality control check in maize hybrid breeding, variety release and seed production. In this study, genetic purity, parent-offspring relationship and diversity among the inbred lines were assessed using 92 single-nucleotide polymorphism (SNP) markers. A total of 188 maize genotypes, comprising of 26 inbred lines, four doubled haploid (DH) lines and 158 single-cross maize hybrids were investigated in this study using Kompetitive Allele Specific Polymerase Chain Reaction (KASP) genotyping assays. The bi-allelic data was analyzed for genetic purity and diversity parameters using GenAlex software. The SNP markers were highly polymorphic and 90% had polymorphic information content (PIC) values of > 0.3. Pairwise genetic distances among the lines ranged from 0.05 to 0.56, indicating a high level of dissimilarity among the inbred lines. A maximum genetic distance of (0.56) was observed between inbred lines CKDHL0089 and CML443 while the lowest (0.05) was between I-42 and I-40. The majority (67%) of the inbred lines studied were genetically pure with residual heterozygosity of <5%, while only 33% had heterozygosity levels of >5%. Inbred lines, which were not pure, require purification through further inbreeding. Cluster analysis partitioned the lines into three distinct genetic clusters with the potential to contribute new beneficial alleles to the maize breeding program. Out of the 68 hybrids (43%) that passed the parent-offspring test, seven hybrids namely; SCHP29, SCHP95, SCHP94, SCHP134, SCHP44, SCHP114 and SCHP126, were selected as potential candidates for further evaluation and release due to their outstanding yield performance.

Genome-wide association study identifies loci, beneficial alleles, and candidate genes for cadmium tolerance in castor (Ricinus communis L.)

Cadmium (Cd) is a phytotoxic element that may impede oilseed production. Breeding of Cd-tolerant cultivars is an imperative that can subsequently be used for phytoremediation of Cd-contaminated soils. Hence, to identify marker-trait associations and mine for candidate genes that confer Cd tolerance in castor, genome-wide association study (GWAS) for seven Cdtolerance-related traits was performed using a naturalized population of 175 castor accessions genotyped by 143 polymorphic simple sequence repeat markers. The results showed that there was a wide variation of Cd among the seven traits in the 175 castor accessions. A total of 27 significant (-log10P > 1.5) marker loci were detected to be associated with all the seven traits for Cd tolerance, and the phenotypic variance explained by these loci varied from 5.63∼20.47 %. Mining of beneficial alleles revealed 29 and 181 alleles that contributed prominently to Cd tolerance and sensitivity, respectively, which would be useful for breeding Cd-tolerant cultivars. Eight novel putative candidate genes involved in stress responses and developmental processes were detected within the major loci. Gene expression analyses using the quantitative real-time polymerase chain reaction method on six selected candidate genes showed that all the genes were highly expressed in the tolerant and sensitive accessions under Cd stress, signifying their potential role in enhancing stress tolerance or responses. This study represented the first attempt to GWAS mapping and identification of novel genes in castor under Cd stress. Our results may facilitate the study of the molecular and genetic basis of Cd tolerance and the cloning of candidate Cd-tolerance genes and cultivars, which could be useful for remediation of Cd-contaminated environments.

Combining Ability and Gene Action Controlling Grain Yield and Its Related Traits in Bread Wheat under Heat Stress and Normal Conditions

High temperature is a major environmental stress that devastatingly affects wheat production. Thenceforth, developing heat-tolerant and high-yielding wheat genotypes has become more critical to sustaining wheat production particularly under abrupt climate change and fast-growing global population. The present study aimed to evaluate parental genotypes and their cross combinations under normal and heat stress conditions, exploring their diversity based on dehydration-responsive element-binding 2 gene (DREB, stress tolerance gene in response to abiotic stress) in parental genotypes, and determining gene action controlling yield traits through half-diallel analysis. Six diverse bread wheat genotypes (local and exotic) and their 15 F1 hybrids were evaluated at two different locations under timely and late sowing dates. Sowing date, location, genotype, and their interactions significantly impacted the studied traits; days to heading, chlorophyll content, plant height, grain yield, and its attributes. Cluster analysis classified the parents and their crosses into four groups varying from heat-tolerant to heat-sensitive based on heat tolerance indices. The parental genotypes P2 and P4 were identified as an excellent source of beneficial alleles for earliness and high yielding under heat stress. This was corroborated by DNA sequence analysis of DREB transcription factors. They were the highest homologies for dehydrin gene sequence with heat-tolerant wheat species. The hybrid combinations of P1 × P5, P1 × P6, P2 × P4, and P3 × P5 were detected to be good specific combiners for grain yield and its attributes under heat stress conditions. These designated genotypes could be used in wheat breeding for developing heat-tolerant and climate-resilient cultivars. The non-additive genetic variances were preponderant over additive genetic variances for grain yield and most traits under both sowing dates. The narrow-sense heritability ranged from low to moderate for most traits. Strong positive associations were detected between grain yield and each of chlorophyll content, plant height, number of grains/spike, and thousand-grain weights, which suggest their importance for indirect selection under heat stress, especially in early generations, due to the effortlessness of their measurement.