ABSTRACT
Powdery mildew (PM), caused by Blumeria graminis f. sp. tritici, poses a significant threat to wheat production, necessitating the development of genetically resistant varieties for long-term control. Therefore, exploring genetic architecture of PM in wheat to uncover important genomic regions is an important area of wheat research. In recent years, the utilization of meta-QTL (MQTL) analysis has gained prominence as an essential tool for unraveling the complex genetic architecture underlying complex quantitative traits. The aim of this research was to conduct a QTL meta-analysis to pinpoint the specific genomic regions in wheat responsible for governing PM resistance. This study integrated 222 QTLs from 33 linkage-based studies using a consensus map with 54,672 markers. The analysis revealed 39 MQTLs, refined to 9 high-confidence MQTLs (hcMQTLs) with confidence intervals of 0.49 to 12.94 cM. The MQTLs had an average physical interval of 41.00 Mb, ranging from 0.000048 Mb to 380.71 Mb per MQTL. Importantly, 18 MQTLs co-localized with known resistance genes like Pm2, Pm3, Pm8, Pm21, Pm38, and Pm41. The study identified 256 gene models within hcMQTLs, providing potential targets for marker-assisted breeding and genomic prediction programs to enhance PM resistance. These MQTLs would serve as a foundation for fine mapping, gene isolation, and functional genomics studies, facilitating a deeper understanding of molecular mechanisms. The identification of candidate genes opens up exciting possibilities for the development of PM-resistant wheat varieties after validation.
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BACKGROUND: Rice bean (Vigna umbellata), an underrated legume, adapts to diverse climatic conditions with the potential to support food and nutritional security worldwide. It is used as a vegetable, minor food crop and a fodder crop, being a rich source of proteins, minerals, and essential fatty acids. However, little effort has been made to decipher the genetic and molecular basis of various useful traits in this crop. Therefore, we considered three economically important traits i.e., flowering, maturity and seed weight of rice bean and identified the associated candidate genes employing an associative transcriptomics approach on 100 diverse genotypes out of 1800 evaluated rice bean accessions from the Indian National Genebank. RESULTS: The transcriptomics-based genotyping of one-hundred diverse rice bean cultivars followed by pre-processing of genotypic data resulted in 49,271 filtered markers. The STRUCTURE, PCA and Neighbor-Joining clustering of 100 genotypes revealed three putative sub-populations. The marker-trait association analysis involving various genome-wide association study (GWAS) models revealed significant association of 82 markers on 48 transcripts for flowering, 26 markers on 22 transcripts for maturity and 22 markers on 21 transcripts for seed weight. The transcript annotation provided information on the putative candidate genes for the considered traits. The candidate genes identified for flowering include HSC80, P-II PsbX, phospholipid-transporting-ATPase-9, pectin-acetylesterase-8 and E3-ubiquitin-protein-ligase-RHG1A. Further, the WRKY1 and DEAD-box-RH27 were found to be associated with seed weight. Furthermore, the associations of PIF3 and pentatricopeptide-repeat-containing-gene with maturity and seed weight, and aldo-keto-reductase with flowering and maturity were revealed. CONCLUSION: This study offers insights into the genetic basis of key agronomic traits in rice bean, including flowering, maturity, and seed weight. The identified markers and associated candidate genes provide valuable resources for future exploration and targeted breeding, aiming to enhance the agronomic performance of rice bean cultivars. Notably, this research represents the first transcriptome-wide association study in pulse crop, uncovering the candidate genes for agronomically useful traits.
Subject(s)
Flowers , Genome-Wide Association Study , Seeds , Transcriptome , Seeds/genetics , Seeds/growth & development , Flowers/genetics , Flowers/growth & development , Vigna/genetics , Vigna/growth & development , Genes, Plant , Genotype , Gene Expression Profiling , Chromosome Mapping , Quantitative Trait Loci/genetics , PhenotypeABSTRACT
Landraces are important genetic resources that have a significant role in maintaining the long-term sustainability of traditional agro-ecosystems, food, nutrition, and livelihood security. In an effort to document landraces in the on-farm conservation context, Central Western Ghat region in India was surveyed. A total of 671 landraces belonging to 60 crops were recorded from 24 sites. The custodian farmers were found to conserve a variety of crops including vegetables, cereals and pulses, perennial fruits, spices, tuber and plantation crops. The survey indicated a difference in the prevalence of landraces across the sites. A significant difference with respect to the Shannon-diversity index, Gini-Simpson index, evenness, species richness, and abundance was observed among the different survey sites. Computation of a prevalence index indicated the need for immediate intervention in the form of collecting and ex situ conservation of landraces of some crops as a back-up to on-farm conservation. The study also identified the critical determinants of on-farm conservation, including (i) suitability to regional conditions, (ii) relevance in regional cuisine and local medicinal practices, (iii) cultural and traditional significance, and (iv) economic advantage. The information documented in this study is expected to promote the collection and conservation of landraces ex situ. The National Genebank housed at ICAR-NBPGR, New Delhi conserves around 550 accessions of landraces collected from the Central Western Ghats region surveyed in this report. Information collected from custodian farmers on specific uses will be helpful to enhance the utilization of these accessions.
Subject(s)
Biodiversity , Conservation of Natural Resources , Crops, Agricultural , Farms , India , Crops, Agricultural/growth & development , Conservation of Natural Resources/methods , Agriculture , Humans , EcosystemABSTRACT
BACKGROUND: Wheat rusts are important biotic stresses, development of rust resistant cultivars through molecular approaches is both economical and sustainable. Extensive phenotyping of large mapping populations under diverse production conditions and high-density genotyping would be the ideal strategy to identify major genomic regions for rust resistance in wheat. The genome-wide association study (GWAS) population of 280 genotypes was genotyped using a 35 K Axiom single nucleotide polymorphism (SNP) array and phenotyped at eight, 10, and, 10 environments, respectively for stem/black rust (SR), stripe/yellow rust (YR), and leaf/brown rust (LR). RESULTS: Forty-one Bonferroni corrected marker-trait associations (MTAs) were identified, including 17 for SR and 24 for YR. Ten stable MTAs and their best combinations were also identified. For YR, AX-94990952 on 1A + AX-95203560 on 4A + AX-94723806 on 3D + AX-95172478 on 1A showed the best combination with an average co-efficient of infection (ACI) score of 1.36. Similarly, for SR, AX-94883961 on 7B + AX-94843704 on 1B and AX-94883961 on 7B + AX-94580041 on 3D + AX-94843704 on 1B showed the best combination with an ACI score of around 9.0. The genotype PBW827 have the best MTA combinations for both YR and SR resistance. In silico study identifies key prospective candidate genes that are located within MTA regions. Further, the expression analysis revealed that 18 transcripts were upregulated to the tune of more than 1.5 folds including 19.36 folds (TraesCS3D02G519600) and 7.23 folds (TraesCS2D02G038900) under stress conditions compared to the control conditions. Furthermore, highly expressed genes in silico under stress conditions were analyzed to find out the potential links to the rust phenotype, and all four genes were found to be associated with the rust phenotype. CONCLUSION: The identified novel MTAs, particularly stable and highly expressed MTAs are valuable for further validation and subsequent application in wheat rust resistance breeding. The genotypes with favorable MTA combinations can be used as prospective donors to develop elite cultivars with YR and SR resistance.
Subject(s)
Basidiomycota , Disease Resistance , Genome-Wide Association Study , Plant Diseases , Polymorphism, Single Nucleotide , Triticum , Triticum/genetics , Triticum/microbiology , Plant Diseases/microbiology , Plant Diseases/genetics , Disease Resistance/genetics , Basidiomycota/physiology , Phenotype , Genes, Plant , Genotype , Puccinia/physiology , Quantitative Trait LociABSTRACT
Sesame (Sesamum indicum L.) is an ancient oilseed crop belonging to the family Pedaliaceae and a globally cultivated crop for its use as oil and food. In this study, 2496 sesame accessions, being conserved at the National Genebank of ICAR-National Bureau of Plant Genetic Resources (NBPGR), were genotyped using genomics-assisted double-digest restriction-associated DNA sequencing (ddRAD-seq) approach. A total of 64,910 filtered single-nucleotide polymorphisms (SNPs) were utilized to assess the genome-scale diversity. Applications of this genome-scale information (reduced representation using restriction enzymes) are demonstrated through the development of a molecular core collection (CC) representing maximal SNP diversity. This information is also applied in developing a mid-density panel (MDP) comprising 2515 hyper-variable SNPs, representing almost equally the genic and non-genic regions. The sesame CC comprising 384 accessions, a representative set of accessions with maximal diversity, was identified using multiple criteria such as k-mer (subsequence of length "k" in a sequence read) diversity, observed heterozygosity, CoreHunter3, GenoCore, and genetic differentiation. The coreset constituted around 15% of the total accessions studied, and this small subset had captured >60% SNP diversity of the entire population. In the coreset, the admixture analysis shows reduced genetic complexity, increased nucleotide diversity (π), and is geographically distributed without any repetitiveness in the CC germplasm. Within the CC, India-originated accessions exhibit higher diversity (as expected based on the center of diversity concept), than those accessions that were procured from various other countries. The identified CC set and the MDP will be a valuable resource for genomics-assisted accelerated sesame improvement program.
Subject(s)
Polymorphism, Single Nucleotide , Sesamum , Sesamum/genetics , Sequence Analysis, DNA , Genotyping Techniques , Genome, Plant , Genotype , DNA, Plant/geneticsABSTRACT
Andrographis paniculata (Burm. f.) Nees is an important medicinal plant known for its bioactive compound andrographolide. NAC transcription factors (NAM, ATAF1/2, and CUC2) play a crucial role in secondary metabolite production, stress responses, and plant development through hormonal signaling. In this study, a putative partial transcript of three NAC family genes (ApNAC83, ApNAC21 22 and ApNAC02) was used to isolate full length genes using RACE. Bioinformatics analyses such as protein structure prediction, cis-acting regulatory elements, and gene ontology analysis were performed. Based on in silico predictions, the diterpenoid profiling of the plant's leaves (five-week-old) and the real-time PCR-based expression analysis of isolated NAC genes under abscisic acid (ABA) treatment were performed. Additionally, the expression analysis of isolated NAC genes under MeJA treatment and transient expression in Nicotiana tabacum was performed. Full-length sequences of three members of the NAC transcription factor family, ApNAC83 (1102 bp), ApNAC21 22 (996 bp), and ApNAC02 (1011 bp), were isolated and subjected to the promoter and gene ontology analysis, which indicated their role in transcriptional regulation, DNA binding, ABA-activated signaling, and stress management. It was observed that ABA treatment leads to a higher accumulation of andrographolide and 14-deoxyandrographolide content, along with the upregulation of ApNAC02 (9.6-fold) and the downregulation of ApNAC83 and ApNAC21 22 in the leaves. With methyl jasmonate treatment, ApNAC21 22 expression decreased, while ApNAC02 increased (1.9-fold), with no significant change being observed in ApNAC83. The transient expression of the isolated NAC genes in a heterologous system (Nicotiana benthamiana) demonstrated their functional transcriptional activity, leading to the upregulation of the NtHMGR gene, which is related to the terpene pathway in tobacco. The expression analysis and heterologous expression of ApNAC21 22 and ApNAC02 indicated their role in andrographolide biosynthesis.
Subject(s)
Acetates , Andrographis , Cyclopentanes , Diterpenes , Gene Expression Regulation, Plant , Oxylipins , Plant Proteins , Transcription Factors , Diterpenes/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Andrographis/genetics , Andrographis/metabolism , Nicotiana/genetics , Nicotiana/metabolism , Phylogeny , Abscisic Acid/metabolism , Abscisic Acid/pharmacology , Plant Leaves/genetics , Plant Leaves/metabolismABSTRACT
Amaranthus is a genus of C4 dicotyledonous herbaceous plant species that are widely distributed in Asia, Africa, Australia, and Europe and are used as grain, vegetables, forages, and ornamental plants. Amaranth species have gained significant attention nowadays as potential sources of nutritious food and industrial products. In this study, we performed a comparative genome analysis of five amaranth species, namely, Amaranthus hypochondriacus, Amaranthus tuberculatus, Amaranthus hybridus, Amaranthus palmeri, and Amaranthus cruentus. The estimated repeat content ranged from 54.49% to 63.26% and was not correlated with the genome sizes. Out of the predicted repeat classes, the majority of repetitive sequences were Long Terminal Repeat (LTR) elements, which account for about 13.91% to 24.89% of all amaranth genomes. Phylogenetic analysis based on 406 single-copy orthologous genes revealed that A. hypochondriacus is most closely linked to A. hybridus and distantly related to A. cruentus. However, dioecious amaranth species, such as A. tuberculatus and A. palmeri, which belong to the subgenera Amaranthus Acnida, have formed their distinct clade. The comparative analysis of genomic data of amaranth species will be useful to identify and characterize agronomically important genes and their mechanisms of action. This will facilitate genomics-based, evolutionary studies, and breeding strategies to design faster, more precise, and predictable crop improvement programs.
ABSTRACT
BACKGROUND: Rice (Oryza sativa L.) is one of the globally important staple food crops, and yield-related traits are prerequisites for improved breeding efficiency in rice. Here, we used six different genome-wide association study (GWAS) models for 198 accessions, with 553,229 single nucleotide markers (SNPs) to identify the quantitative trait nucleotides (QTNs) and candidate genes (CGs) governing rice yield. RESULTS: Amongst the 73 different QTNs in total, 24 were co-localized with already reported QTLs or loci in previous mapping studies. We obtained fifteen significant QTNs, pathway analysis revealed 10 potential candidates within 100kb of these QTNs that are predicted to govern plant height, days to flowering, and plot yield in rice. Based on their superior allelic information in 20 elite and 6 inferior genotypes, we found a higher percentage of superior alleles in the elite genotypes in comparison to inferior genotypes. Further, we implemented expression analysis and enrichment analysis enabling the identification of 73 candidate genes and 25 homologues of Arabidopsis, 19 of which might regulate rice yield traits. Of these candidate genes, 40 CGs were found to be enriched in 60 GO terms of the studied traits for instance, positive regulator metabolic process (GO:0010929), intracellular part (GO:0031090), and nucleic acid binding (GO:0090079). Haplotype and phenotypic variation analysis confirmed that LOC_OS09G15770, LOC_OS02G36710 and LOC_OS02G17520 are key candidates associated with rice yield. CONCLUSIONS: Overall, we foresee that the QTNs, putative candidates elucidated in the study could summarize the polygenic regulatory networks controlling rice yield and be useful for breeding high-yielding varieties.
Subject(s)
Genome-Wide Association Study , Oryza , Chromosome Mapping , Oryza/genetics , Plant Breeding , Quantitative Trait Loci/geneticsABSTRACT
The study was conducted to identify novel simple sequence repeat (SSR) markers associated with resistance to corn aphid (CLA), Rhopalosiphum maidis L. in 48 selected bread wheat (Triticum aestivum L.) and wild wheat (Aegilops spp. & T. dicoccoides) genotypes during two consecutive cropping seasons (2018-19 and 2019-20). A total of 51 polymorphic markers containing 143 alleles were used for the analysis. The frequency of the major allele ranged from 0.552 (Xgwm113) to 0.938 (Xcfd45, Xgwm194 and Xgwm526), with a mean of 0.731. Gene diversity ranged from 0.116 (Xgwm526) to 0.489 (Xgwm113), with a mean of 0.354. The polymorphic information content (PIC) value for the SSR markers ranged from 0.107 (Xgwm526) to 0.370 (Xgwm113) with a mean of 0.282. The results of the STRUCTURE analysis revealed the presence of four main subgroups in the populations. Analysis of molecular variance (AMOVA) showed that the between-group difference was around 37 per cent of the total variation contributed to the diversity by the whole germplasm, while 63 per cent of the variation was attributed between individuals within the group. A general linear model (GLM) was used to identify marker-trait associations, which detected a total of 23 and 27 significant new marker-trait associations (MTAs) at the p < 0.01 significance level during the 2018-19 and 2019-20 crop seasons, respectively. The findings of this study have important implications for the identification of molecular markers associated with CLA resistance. These markers can increase the accuracy and efficiency of aphid-resistant germplasm selection, ultimately facilitating the transfer of resistance traits to desirable wheat genotypes.
Subject(s)
Aphids , Triticum , Humans , Animals , Triticum/genetics , Aphids/genetics , Zea mays/genetics , Genetic Variation , Microsatellite Repeats/geneticsABSTRACT
Spot blotch caused by Bipolaris sorokiniana ((Sacc.) Shoemaker) (teleomorph: Cochliobolus sativus [Ito and Kuribayashi] Drechsler ex Dastur) is an economically important disease of warm and humid regions. The present study focused on identifying resistant genotypes and single-nucleotide polymorphism (SNP) markers associated with spot blotch resistance in a panel of 174 bread spring wheat lines using field screening and genome-wide association mapping strategies. Field experiments were conducted in Agua Fria, Mexico, during the 2019-2020 and 2020-2021 cropping seasons. A wide range of phenotypic variation was observed among genotypes tested during both years. Twenty SNP markers showed significant association with spot blotch resistance on 15 chromosomes, namely, 1A, 1B, 2A, 2B, 2D, 3A, 3B, 4B, 4D, 5A, 5B, 6A, 6B, 7A, and 7B. Of these, two consistently significant SNPs on 5A, TA003225-0566 and TA003225-1427, may represent a new resistance quantitative trait loci. Further, in the proximity of Tsn1 on 5B, AX-94435238 was the most stable and consistent in both years. The identified genomic regions could be deployed to develop spot blotch-resistant genotypes, particularly in the spot blotch-vulnerable wheat growing areas.
Subject(s)
Bipolaris , Genome-Wide Association Study , Triticum , Triticum/genetics , Seasons , Phenotype , Disease Resistance/genetics , Plant Diseases/genetics , GenotypeABSTRACT
Moth bean (Vigna aconitifolia), a drought and heat-resistant legume from the Fabaceae family, is commonly cultivated in arid and semi-arid regions of the Indian subcontinent In September 2022, phyllody symptoms (Figure 1) were observed on 50-days-old moth bean plants at the ICAR-NBPGR research farm in Jodhpur, Rajasthan, India. The disease incidence ranged from 10 to 25%. To investigate the cause, ten symptomatic VacoJod (1-10) and ten asymptomatic VacoJod (11-20) Vigna aconitifolia plants were collected. Insect populations were also collected from the vicinity using the sweep-net method to examine the role of insect vectors. The leafhopper was identified based on morphological characterization as Empoasca sp. at the Division of Entomology, ICAR-IARI, New Delhi. DNA was extracted from midribs of all collected plants and the Empoasca sp., using Qiagen DNeasy Plant Mini Kit and Blood and Tissue kit, respectively. Nested polymerase chain reaction (Nested-PCR) with universal primers P1/P7 and R16F2n/R16R2 (Deng and Hiruki, 1991; Gundersen and Lee, 1996), and secA gene primers (secAfor1/secArev3 and secAfor2/secArev3) (Hodgetts et al., 2008) were employed to determine phytoplasma species association. Out of the 10 symptomatic plants and 10 leafhopper samples, 6 leafhopper samples and all symptomatic plants produced expected band sizes for the 16S rRNA (approximately 1.25 kb) and secA gene (480 bp). The PCR products were cloned, sequenced, and sequences (two each from moth bean and leafhopper) were submitted to NCBI GenBank with accession numbers OP941130, OP941132, OP941133 and OP941134 for 16S rRNA and OP958868, OP958869, OP958870, and OP958871 for secA gene sequences. Nucleotide BLAST analysis of 16S rRNA sequences revealed a minimum of 99.92% similarity with 'Primula acaulis' yellows phytoplasma (KJ494340) from Czech Republic. All 100% hits corresponded to 16SrI-B group phytoplasmas, for example rapeseed phyllody phytoplasma (CP055264) from Taiwan. Similarly, nucleotide BLAST analysis of secA sequences revealed a minimum of 99.15% sequence similarity with Paulownia witches'-broom phytoplasma (secA) (OP124308) from China. All 100% hits were of 16SrI-B group phytoplasmas, for example Ageratum conyzoides yellowing phytoplasma (MW401697, secA) from India. Phylogenetic analysis using MEGA11 (Tamura et al., 2021) clustered the moth bean and Empoasca sp. phytoplasma strains with 16SrI-B phytoplasma reference strains. iPhyClassifier tool classified the 16S rRNA gene sequences into 16Sr group I, subgroup B, with a similarity coefficient of 1.0 (Figure 2a, 2b). This marks the first report of the association of 'Ca. P. asteris' 16SrI-B related phytoplasma strain with moth bean plants globally. The 16SrI-B phytoplasma strain is prevalent in various crops in India (Singh et al., 2023). This report emphasizes the epidemiological studies and highlights the need for further research and preventive measures to manage the spread of this phytoplasma strain, which could impact crop production and food security in hot and dry regions.
ABSTRACT
Wheat, an important cereal crop globally, faces major challenges due to increasing global population and changing climates. The production and productivity are challenged by several biotic and abiotic stresses. There is also a pressing demand to enhance grain yield and quality/nutrition to ensure global food and nutritional security. To address these multifaceted concerns, researchers have conducted numerous meta-QTL (MQTL) studies in wheat, resulting in the identification of candidate genes that govern these complex quantitative traits. MQTL analysis has successfully unraveled the complex genetic architecture of polygenic quantitative traits in wheat. Candidate genes associated with stress adaptation have been pinpointed for abiotic and biotic traits, facilitating targeted breeding efforts to enhance stress tolerance. Furthermore, high-confidence candidate genes (CGs) and flanking markers to MQTLs will help in marker-assisted breeding programs aimed at enhancing stress tolerance, yield, quality and nutrition. Functional analysis of these CGs can enhance our understanding of intricate trait-related genetics. The discovery of orthologous MQTLs shared between wheat and other crops sheds light on common evolutionary pathways governing these traits. Breeders can leverage the most promising MQTLs and CGs associated with multiple traits to develop superior next-generation wheat cultivars with improved trait performance. This review provides a comprehensive overview of MQTL analysis in wheat, highlighting progress, challenges, validation methods and future opportunities in wheat genetics and breeding, contributing to global food security and sustainable agriculture.
Subject(s)
Plant Breeding , Triticum , Triticum/genetics , Plant Breeding/methods , Quantitative Trait Loci , Phenotype , Crops, Agricultural/genetics , Edible Grain/geneticsABSTRACT
Introduction: The introgression of genetic material from one species to another through wide hybridization and repeated back-crossing, plays an important role in genetic modification and enriching the cultivated gene-pool with novel genetic variations. Okra (Abelmoschus esculentus [(L.) Moench)] is a popular vegetable crop with high dietary fibre and protein, rich in essential amino acids, lysine and tryptophan. The wild Abelmoschus genepool has many desirable traits like ornamental value, short internodal length, more number of productive branches, extended bearing, perennation tendency, reduced fruit length (more consumer preferred trait), high mucilage content (medicinal value), abiotic stress tolerances such as drought, high temperature and biotic stress resistances such as okra Yellow Vein Mosaic Virus (YVMV) and Enation Leaf Curl Virus (ELCV) diseases. The repeated use of elite breeding lines led to narrowing of the genetic base of the okra crop, one of the major factors attributed to breakdown of resistance/ tolerance to biotic stresses. YVMV and ELCV are the two major diseases, causing significant yield loss in okra. Hence, wide hybridization was attempted to transfer tolerance genes from wild species to the cultivated genepool to widen the genetic base. Material and methods: The screening of germplasm of wild Abelmoschus species at hotspots led to the identification of tolerant species (Abelmoschus pungens var. mizoramensis, A. enbeepeegeearensis, A. caillei, A. tetraphyllus and A. angulosus var. grandiflorus), which were further used in a wide-hybridization programme to generate interspecific hybrids with the cultivated okra. Presence of pre- and post-zygotic barriers to interspecific geneflow, differences in ploidy levels and genotype specific variations in chromosome numbers led to varying degrees of sterility in F1 plants of interspecific crosses. This was overcome by doubling the chromosome number of interspecific hybrids by applying Colchicine at the seedling stage. The 113 cross derivatives generated comprising amphidiploids in the F1 generation (30), F3 (14), one each in F2 and F4 generations, back cross generation in BC1F2 (03), BC1F3 (25), and BC2F3 (02), crosses between amphidiploids (27), multi-cross combinations (07) and inter-specific cross (between A. sagittifolius × A. moschatus subsp. moschatus) selfed derivatives at F8 generation (03) were characterized in the present study. Besides they were advanced through selfing and backcrossing. Results and Discussion: The amphidiploids were found to possess many desirable genes with a considerable magnitude of linkage drag. Majority of the wide cross derivatives had an intermediate fruit morphology and dominance of wild characters viz., hispid fruits, stem, leaves, tough fruit fibre, vigorous perennial growth habit and prolonged flowering and fruiting. The fruit morphology of three BC progenies exhibited a high morphological resemblance to the cultivated okra, confirming successful transfer of useful genes to the cultivated okra genepool. The detailed morphological characteristics of the various combinations of Abelmoschus amphidiploids and the genetic enhancement of the genepool achieved in this process is reported here.
ABSTRACT
The leaf blight diseases, Septoria nodorum blotch (SNB), and tan spot (TS) are emerging due to changing climatic conditions in the northern parts of India. We screened 296 bread wheat cultivars released in India over the past 20 years for seedling resistance against SNB (three experiments) and TS (two experiments). According to a genome-wide association study, six QTLs on chromosome arms 1BL, 2AS, 5BL, and 6BL were particularly significant for SNB across all three years, of which Q.CIM.snb.1BL, Q.CIM.snb.2AS1, Q.CIM.snb.2AS.2, and Q.CIM.snb.6BL appeared novel. In contrast, those on 5BS and 5BL may correspond to Snn3 and Tsn1, respectively. The allelic combination of tsn1/snn3 conferred resistance to SNB, whereas that of Tsn1/Snn3 conferred high susceptibility. As for TS, Tsn1 was the only stably significant locus identified in this panel. Several varieties like PBW 771, DBW 277, and HD 3319, were identified as highly resistant to both diseases that can be used in future wheat improvement programs as resistant donors.
ABSTRACT
Corn-leaf aphid (CLA-Rhopalosiphum maidis) is a major insect pest of barley (Hordeum vulgare) causing yield loss upto 30% under severe infestation. Keeping in view of the availability of very few sources of CLA resistance in barley, the present investigation was framed to assess the genetic diversity and population structure of 43 wild barley (H. vulgare subsp. spontaneum) genotypes using eight microsatellite markers against R. maidis. Three statistical methods viz. multivariate-hierarchical clustering, Bayesian clustering and PCoA, unanimously grouped genotypes into three subpopulations (K = 3) with 25.58% (SubPop1-Red), 39.53% (SubPop2-Green) and 34.88% (SubPop3-Blue) genotypes including admixtures. Based on Q ≥ 66.66%, 37.20% genotypes formed a superficial "Mixed/Admixture" subpopulation. All polymorphic SSR markers generated 36 alleles, averaging to 4.5 alleles/locus (2-7 range). The PIC and H were highest in MS31 and lowest in MS28, with averages of 0.66 and 0.71. MAF and mean genetic diversity were 0.16 and 89.28%, respectively. All these parameters indicated the presence of predominant genetic diversity and population structure amongst the studied genotypes. Based on AII, only 6 genotypes were found to be R. maidis resistant. SubPop3 had 91.66% (11) of the resistant or moderately resistant genotypes. SubPop3 also had the most pure genotypes (11), the least aphid infestation (8.78), and the highest GS (0.88), indicating its suitability for future R. maidis resistance breeding initiatives.
Subject(s)
Aphids , Hordeum , Animals , Hordeum/genetics , Aphids/genetics , Zea mays/genetics , Bayes Theorem , Plant Breeding , Plant Leaves , Genetic VariationABSTRACT
Corn-leaf aphid (CLA), Rhopalosiphum maidis (Fitch) (Hemiptera: Aphididae) is a serious economic pest of barley worldwide. Breeding for aphid resistance in plants is considered a cost-effective and environmentally safe approach for aphid control, compared to the use of chemical pesticides. One of the challenges in breeding for aphid resistance is the identification of resistant plant genotypes, which can be achieved through the use of molecular markers. In the present study, a set of aphid specific 10 simple-sequence repeats (SSR) markers were used to investigate genetic diversity and population structure analyses in 109 barley genotypes against R. maidis. Three statistical methods viz., multivariate hierarchical clustering based on Jaccard's similarity coefficient, principal coordinate analysis (PCoA) and the Bayesian approach were utilized to classify the 109 barley genotypes. The analyses revealed four subpopulations i.e., SubPop1, SubPop2, SubPop3 and SubPop4 with 19, 46, 20 and 24 genotypes including admixtures, respectively and represented 17.43%, 42.2%, 18.34% and 22.01% genotypes of the total population size, respectively. The studied SSR markers produced 67 polymorphic bands, with an average of 6.7 and ranging from 3 to 12 bands. Heterozygosity (H) was found to be highest in SSR28 (0.64) and lowest in SSR27 (0.89). The observed genetic diversity index varied from 0.10 to 0.34 (with an average of 0.19). Major allele frequency varied from 74.08% to 94.80%. On an average, 87.52% of the 109 barley genotypes shared a common major allele at any locus. Based on the Aphid Infestation Index (AII), only 2 genotypes were found to be resistant against CLA. SubPop2 also had lowest mean aphid population (28.83), widest genetic similarity index (0.60-1.00) and highest genetic similarity coefficient (0.82), which highlighted its potential for inclusion in future CLA resistance breeding programs.
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Wheat crop is subjected to various biotic and abiotic stresses, which affect crop productivity and yield. Among various abiotic stresses, drought stress is a major problem considering the current global climate change scenario. A high-yielding wheat variety, HD3086, has been released for commercial cultivation under timely sown irrigated conditions for the North Western Plain Zone (NWPZ) and North Eastern Plain Zone NEPZ of India. Presently, HD3086 is one of the highest breeder seed indented wheat varieties and has a stable yield over the years. However, under moisture deficit conditions, its potential yield cannot be achieved. The present study was undertaken to transfer drought-tolerant QTLs in the background of the variety HD3086 using marker-assisted backcross breeding. QTLs governing Biomass (BIO), Canopy Temperature (CT), Thousand Kernel Weight (TKW), Normalized Difference Vegetation Index (NDVI), and Yield (YLD) were transferred to improve performance under moisture deficit conditions. In BC1F1, BC2F1, and BC2F2 generations, the foreground selection was carried out to identify the plants with positive QTLs conferring drought tolerance and linked to traits NDVI, CT, TKW, and yield. The positive homozygous lines for targeted QTLs were advanced from BC2F2 to BC2F4 via the pedigree-based phenotypic selection method. Background analysis was carried out in BC2F5 and obtained 78-91% recovery of the recurrent parent genome in the improved lines. Furthermore, the advanced lines were evaluated for 2 years under drought stress to assess improvement in MABB-derived lines. Increased GWPS, TKW, and NDVI and reduced CT was observed in improved lines. Seven improved lines were identified with significantly higher yields in comparison to HD3086 under stress conditions.
ABSTRACT
Wheat (Triticum aestivum L.) is a staple food crop for the global human population, and thus wheat breeders are consistently working to enhance its yield worldwide. In this study, we utilized a sub-set of Indian wheat mini core germplasm to underpin the genetic architecture for seed shape-associated traits. The wheat mini core subset (125 accessions) was genotyped using 35K SNP array and evaluated for grain shape traits such as grain length (GL), grain width (GW), grain length, width ratio (GLWR), and thousand grain weight (TGW) across the seven different environments (E1, E2, E3, E4, E5, E5, E6, and E7). Marker-trait associations were determined using a multi-locus random-SNP-effect Mixed Linear Model (mrMLM) program. A total of 160 non-redundant quantitative trait nucleotides (QTNs) were identified for four grain shape traits using two or more GWAS models. Among these 160 QTNs, 27, 36, 38, and 35 QTNs were associated for GL, GW, GLWR, and TGW respectively while 24 QTNs were associated with more than one trait. Of these 160 QTNs, 73 were detected in two or more environments and were considered reliable QTLs for the respective traits. A total of 135 associated QTNs were annotated and located within the genes, including ABC transporter, Cytochrome450, Thioredoxin_M-type, and hypothetical proteins. Furthermore, the expression pattern of annotated QTNs demonstrated that only 122 were differentially expressed, suggesting these could potentially be related to seed development. The genomic regions/candidate genes for grain size traits identified in the present study represent valuable genomic resources that can potentially be utilized in the markers-assisted breeding programs to develop high-yielding varieties.
ABSTRACT
BACKGROUND: Moth bean (Vigna aconitifolia) is an underutilized, protein-rich legume that is grown in arid and semi-arid areas of south Asia and is highly resistant to abiotic stresses such as heat and drought. Despite its economic importance, the crop remains unexplored at the genomic level for genetic diversity and trait mapping studies. To date, there is no report of SNP marker discovery and association mapping of any trait in this crop. Therefore, this study aimed to dissect the genetic diversity, population structure and marker-trait association for the flowering trait in a diversity panel of 428 moth bean accessions using genotyping by sequencing (GBS) approach. RESULTS: A total of 9078 high-quality single nucleotide polymorphisms (SNPs) were discovered by genotyping of 428 moth bean accessions. Model-based structure analysis and PCA grouped the moth bean accessions into two subpopulations. Cluster analysis revealed accessions belonging to the Northwestern region of India had higher variability than accessions from the other regions suggesting that this region represents its center of diversity. AMOVA revealed more variations within individuals (74%) and among the individuals (24%) than among the populations (2%). Marker-trait association analysis using seven multi-locus models including mrMLM, FASTmrEMMA FASTmrEMMA, ISIS EM-BLASSO, MLMM, BLINK and FarmCPU revealed 29 potential genomic regions for the trait days to 50% flowering, which were consistently detected in three or more models. Analysis of the allelic effect of the major genomic regions explaining phenotypic variance of more than 10% and those detected in at least 2 environments showed 4 genomic regions with significant phenotypic effect on this trait. Further, we also analyzed genetic relationships among the Vigna species using SNP markers. The genomic localization of moth bean SNPs on genomes of closely related Vigna species demonstrated that maximum numbers of SNPs were getting localized on Vigna mungo. This suggested that the moth bean is most closely related to V. mungo. CONCLUSION: Our study shows that the north-western regions of India represent the center of diversity of the moth bean. Further, the study revealed flowering-related genomic regions/candidate genes which can be potentially exploited in breeding programs to develop early-maturity moth bean varieties.
Subject(s)
Genome-Wide Association Study , Vigna , Vigna/genetics , Genotype , Plant Breeding , Polymorphism, Single Nucleotide/geneticsABSTRACT
Marker-assisted backcross breeding enables selective insertion of targeted traits into the genome to improve yield, quality, and stress resistance in wheat. In the current investigation, we transferred four drought tolerance quantitative trait loci (QTLs) controlling traits, viz canopy temperature, normalized difference vegetative index, chlorophyll content, and grain yield from the drought-tolerant donor line, C306, into a popular high-yielding, drought-sensitive variety, HD2733. Marker-assisted selection coupled with stringent phenotypic screening was used to advance each generation. This study resulted in 23 improved lines carrying combinations of four drought tolerance QTLs with a range of 85.35%-95.79% background recovery. The backcross-derived lines gave a higher yield under moisture-deficit stress conditions compared with the recipient parent. They also showed higher phenotypic mean values for physiological traits and stability characteristics of HD2733. A promising genotype, HD3411, derived from this cross was identified for release after national multi-location coordinating trials under the All India Coordinated Wheat Improvement Project. Our study is a prime example of the advantages of precision breeding using integrating markers and phenotypic selection to develop new cultivars with desirable traits like drought tolerance.