Modern wheat shows phenomenal evolutional success and adaptability to a range of environments owing to polyploidization; however, during its hybridization process a major genetic gain has been ...overlooked. Recently, Gaurav et al. emphasized harnessing genetic diversity from wheat wild progenitor Aegilops tauschii for the improvement of hexaploid wheat through introgression or transgenesis.
Definition of the specific germline immunoglobulin (Ig) alleles present in an individual is a critical first step to delineate the ontogeny and evolution of antigen-specific antibody responses. ...Rhesus and cynomolgus macaques are important animal models for pre-clinical studies, with four main sub-groups being used: Indian- and Chinese-origin rhesus macaques and Mauritian and Indonesian cynomolgus macaques. We applied the (Ig) gene inference tool IgDiscover and performed extensive Sanger sequencing-based genomic validation to define germline VDJ alleles in these 4 sub-groups, comprising 45 macaques in total. There was allelic overlap between Chinese- and Indian-origin rhesus macaques and also between the two macaque species, which is consistent with substantial admixture. The island-restricted Mauritian cynomolgus population displayed the lowest number of alleles of the sub-groups, yet maintained high individual allelic diversity. These comprehensive databases of germline IGH alleles for rhesus and cynomolgus macaques provide a resource toward the study of B cell responses in these important pre-clinical models.
Display omitted
•Macaque germline gene inference identifies several hundred novel IGV alleles•Rhesus and cynomolgus macaques display overlapping IGV allelic content•Analysis of macaque IGV germline genes suggests frequent structural variation•Comprehensive IG databases are essential for analysis of somatic hypermutation
Rhesus and cynomolgus macaques are valuable model organisms for immunological research. Due to the technical difficulties of sequencing the IG loci, the current IG germline gene databases are limited. We applied germline gene inference of expressed antibody repertoires generating comprehensive IGH databases for key sub-groups, furthering genetic analyses of B lymphocyte responses in these species.
The rhesus macaque is a critically important animal model in biomedical research, most recently playing a key role in the development of vaccines against human immunodeficiency virus-1. Nevertheless, ...the immunoglobulin (Ig) loci of macaques are as yet incompletely determined and our understanding of differences between human and macaque humoral immunity remains deficient. We completed a high-coverage, high-quality whole genome sequencing and assembly project with a single rhesus macaque of Indian origin, and partial genome assemblies using genomic molecular targeting of the Ig loci in nine other rhesus macaques of Indian origin. These data indicate that the macaque Ig loci are substantially more diverse than those in humans, including greater sequence diversity and copy-number variation between individuals. It appears likely that such copy-number variation even occurs between allelic loci within individuals. Different Ig gene families in the macaque show distinct relationships to the corresponding human gene families and appear to evolve under different mechanisms. These results raise intriguing questions about the evolution of antigen receptors in primates but also have important practical implications for the design and interpretation of biomedical studies.
The north-western Indian Himalayas possesses vast diversity in common bean germplasm due to several years of natural adaptation and farmer's selection. Systematic efforts have been made for the first ...time for the characterization and use of this huge diversity for the identification of genes/quantitative trait loci (QTLs) for yield and yield-contributing traits in common bean in India. A core set of 96 diverse common bean genotypes was characterized using 91 genome-wide genomic and genic simple sequence repeat (SSR) markers. The study of genetic diversity led to the identification of 691 alleles ranging from 2 to 21 with an average of 7.59 alleles/locus. The gene diversity (expected heterozygosity,
) varied from 0.31 to 0.93 with an average of 0.73. As expected, the genic SSR markers detected less allelic diversity than the random genomic SSR markers. The traditional clustering and Bayesian clustering (structural analysis) analyses led to a clear cut separation of a core set of 96 genotypes into two distinct groups based on their gene pools (Mesoamerican and Andean genotypes). Genome-wide association mapping for pods/plant, seeds/pod, seed weight, and yield/plant led to the identification of 39 significant marker-trait associations (MTAs) including 15 major, 15 stable, and 13 both major and stable MTAs. Out of 39 MTAs detected, 29 were new MTAs reported for the first time, whereas the remaining 10 MTAs were already identified in earlier studies and therefore declared as validation of earlier results. A set of seven markers was such, which were found to be associated with multiple (two to four) different traits. The important MTAs will be used for common bean molecular breeding programs worldwide for enhancing common bean yield.
The human immunoglobulin heavy-chain (IGH) locus is exceptionally polymorphic, with high levels of allelic and structural variation. Thus, germline IGH genotypes are personal, which may influence ...responses to infection and vaccination. For an improved understanding of inter-individual differences in antibody responses, we isolated SARS-CoV-2 spike-specific monoclonal antibodies from convalescent health care workers, focusing on the IGHV1-69 gene, which has the highest level of allelic variation of all IGHV genes. The IGHV1-69∗20-using CAB-I47 antibody and two similar antibodies isolated from an independent donor were critically dependent on allele usage. Neutralization was retained when reverting the V region to the germline IGHV1-69∗20 allele but lost when reverting to other IGHV1-69 alleles. Structural data confirmed that two germline-encoded polymorphisms, R50 and F55, in the IGHV1-69 gene were required for high-affinity receptor-binding domain interaction. These results demonstrate that polymorphisms in IGH genes can influence the function of SARS-CoV-2 neutralizing antibodies.
Display omitted
•IGH genes with high allelic diversity are used in anti-SARS-CoV-2 antibodies•IGH allele usage can influence the activity of neutralizing antibodies•Cryo-EM analysis confirms the role of germline-encoded residues in antigen binding•IGH genotyping can uncover differences in Ab responses due to allelic variation
The genes and alleles of the antigen receptor loci are highly variable between individuals, which may affect the quality of the immune response to different pathogens. Here, Pushparaj et al. use immunoglobulin genotyping and monoclonal antibody engineering to illustrate how heritable differences in such genes can modulate anti-SARS-CoV-2 antibody function.
Abstract Indian mustard (Brassica juncea) is an important contributor towards edible oil supply in India. Traditional Indian mustard varieties contain high proportion of 18C polyunsaturated fatty ...acids (linoleic and linolenic acids) and large amounts of long-chain monounsaturated FAs, mainly erucic acid, in seeds. Oleate desaturase (FAD2) regulates the composition of 18C PUFAs in cellular membranes and TAG in seed oil. The present study was conducted to gain insight into the allelic diversity of the FAD2 gene in Indian mustard. Analyses of cloned FAD2 genes of three Indian mustard varieties revealed a novel FAD2 gene that has a longer ORF (1167 bp) owing to insertions and several SNPs across its length that distinguish it from the more prevalent native FAD2 gene. Overall, the Indian mustard varieties possess three FAD2 alleles, but there is limited nucleotide diversity among members of each FAD2 type across varieties, suggesting narrow genetic diversity among the varieties examined.
Human T cell receptors (TCRs) are critical for mediating immune responses to pathogens and tumors and regulating self-antigen recognition. Yet, variations in the genes encoding TCRs remain ...insufficiently defined. Detailed analysis of expressed TCR alpha, beta, gamma, and delta genes in 45 donors from four human populations—African, East Asian, South Asian, and European—revealed 175 additional TCR variable and junctional alleles. Most of these contained coding changes and were present at widely differing frequencies in the populations, a finding confirmed using DNA samples from the 1000 Genomes Project. Importantly, we identified three Neanderthal-derived, introgressed TCR regions including a highly divergent TRGV4 variant, which mediated altered butyrophilin-like molecule 3 (BTNL3) ligand reactivity and was frequent in all modern Eurasian population groups. Our results demonstrate remarkable variation in TCR genes in both individuals and populations, providing a strong incentive for including allelic variation in studies of TCR function in human biology.
Display omitted
•Extensive human TCR gene heterogeneity exists in both populations and individuals•TCR gene variations frequently involve coding changes and non-functional alleles•Neanderthal-derived TCR regions are found in some modern human populations•A frequent Neanderthal-derived TRGV4 variant mediates reduced BTNL3 ligand reactivity
T cells are critical for immunological responses to pathogens and malignancies; yet, knowledge of variation in expressed human TCR germline genes is limited. Corcoran et al. reveal large TCR allelic variation, doubling the number of validated alleles, showing that many are population-specific and revealing several that originate from human-Neanderthal interbreeding.
Variation at MHC Class II-DQA locus in riverine and swamp buffaloes (Bubu) has been explored in this study. Through sequencing of buffalo DQA, 48 nucleotide variants identified from 17 individuals, ...reporting 42 novel alleles, including one pseudogene. Individual animal displayed two to seven variants, suggesting the presence of more than two Bubu-DQA loci, as an evidence of extensive duplication. dN values were found to be higher than dS values at peptide binding sites, separately for riverine and swamp buffaloes, indicating locus being under positive selection. Evolutionary analysis revealed numerous trans-species polymorphism with alleles from water buffalo assigned to at least three different loci (Bubu-DQA1, DQA2, DQA3). Alleles of both the sub-species intermixed within the cluster, showing convergent evolution of MHC alleles in bovines. The results thus suggest that both riverine and swamp buffaloes share con-current arrangement of DQA region, comparable to cattle in terms of copy number and population polymorphism.
•Swamp and riverine buffalo allelic diversity at MHC DQA locus documented.•Out of 48 allelic patterns, 42 are novel alleles.•Alleles from water buffalo assigned to three different loci, Bubu-DQA1, DQA2, DQA3.•Duplication of DQA locus identified first time in buffalo.•Trans-species polymorphisms and intermixed alleles within phylogenetic clusters indicate convergent evolution in bovines.
Lodging resistance is one of the vital traits in improving the yield and sustainability of production in rice (Oryza sativa L.). A quantitative trait loci (QTL), SCM2 for enhancing the culm strength ...and increased spikelet number has been reported. In the present study, a diverse collection of 150 accessions from the rice 3K-RG panel were assembled and evaluated for the STRONG CULM2 locus. All the accessions under study showed a normal phenotypic distribution for culm diameter and the allelic diversity analysis for SCM2 resulted in four INDEL’s and 17 SNP’s in both coding and non-coding regions of the genome. Haplotype analysis grouped the entire population into three significant haplotype groups with 114 accessions in H1, 19 accessions in H2 and 17 accessions in H3. Haplotypes were formed using two significant SNP sites viz., 27480778 and 27481339. Dunnett’s test disclosed a significant variation between H1-H2 and H1-H3 haplotypes. Phenotypic evaluation for culm diameter in all the three haplotype groups revealed that the genotypes BR IRGA and PERUNEL in H1, CICA 9 and MOSHI in H2 and KITRANA in H3 possess a maximum culm diameter. H2 and H3 were found to be superior to H1 hence can be utilized for lodging resistance in further breeding programs.
PDF
