Rice yield has attained a plateau and hence the enhancement of grain yield is indispensable to feed the growing population, which could be achieved by the identification of superior alleles in the ...existing germplasm. Any variation in the pleiotropic gene, An-1 (yield gene) leads to enhanced grain number and grain size in rice. Hence, the gene was chosen for analyzing the allelic diversity/haplotype variation with 150 lines of 3K RG panel which revealed that, the gene An-1 has 20 Single Nucleotide Polymorphisms and 10 INDELs encompassing both intronic and exonic regions. The genotypes were divided into four haplotypes in the combination of seven SNPs with the maximum number of genotypes in the first haplotype and the least number of genotypes in fourth haplotype. From the study, H1 was identified as a superior haplotype. The haplo-pheno analysis identified the superior donors viz., SIGARDIS, GENIT and DAMNOEUB KAUN KHMOM harbouring superior haplotype combinations, which may be further utilized in haplotype-based breeding for the development of high yielding rice varieties.
AbstractPollen dispersal is a key evolutionary and ecological process, but the degree to which variation in the density of concurrently flowering conspecific plants (i.e., coflowering density) shapes ...pollination patterns remains understudied. We monitored coflowering density and corresponding pollination patterns of the insect-pollinated palm
in northwestern Ecuador and found that the influence of coflowering density on these patterns was scale dependent: high neighborhood densities were associated with reductions in pollen dispersal distance and gametic diversity of progeny arrays, whereas we observed the opposite pattern at the landscape scale. In addition, neighborhood coflowering density also impacted forward pollen dispersal kernel parameters, suggesting that low neighborhood densities encourage pollen movement and may promote gene flow and genetic diversity. Our work reveals how coflowering density at different spatial scales influences pollen movement, which in turn informs our broader understanding of the mechanisms underlying patterns of genetic diversity and gene flow within populations of plants.
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.
This study evaluated the physiological responses and genetic diversity of selected short-grain aromatic rice landraces of Northern Eastern Ghats of India to multiple abiotic stresses. Results ...revealed that drought, salt and flooding stress remarkably declined plant biomass, relative growth index (RGI), relative water content (RWC), leaf photosynthesis, PSII activity, SPAD relative index, and elevated effect was found in susceptible IR64 (susceptible check) variety. We employed molecular marker analysis to characterize 21 rice genotypes using 32 SSR primers related to drought, flooding and salinity tolerance QTLs. Our analysis suggests significantly high polymorphism (93.12%) in 96 loci. The mean value of polymorphism information content (PIC), marker index (MI) and resolving power (RP) and heterozygosity index (HI) were 0.326, 1.037, 1.558 and 0.420 respectively. The Jaccard’s similarity coefficient ranged from 0.158 to 0.846 with a mean genetic dissimilarity of 0.647. According to neighbor-joining method of clustering, all genotypes were grouped into two major and five sub-clusters which is concurrent with a very broad genetic base (K = 5) obtained with STRUCTURE analysis. Taken together, six aromatic genotypes Basubhoga, Dudhamani, Kalajeera, Laktimachi, Kuyerkuling and Tulasi are genetically very close to drought-tolerant (N22) and flooding tolerant (FR13A) cultivar whereas, salt-tolerant (Pokkali) very close to Sapuri and Muktabali. The degree of genetic variants obtained from this profiling could be useful for landrace conservation, selection and global implications for multiple abiotic stress tolerance.
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•Physiological and molecularassessment was carried in aromatic rice germplasms for multiple stress tolerance.•Drought, salt and flooding remarkably declined relative growth index leaf photosynthesis and PSII activity.•Based on STRUCTURE analysis, diversity of 21 rice genotypes was grouped into 5 populations.•The identified rice landraces are the important genetic resources for multiple stress tolerance breeding program.•These genotypes could be useful for germplasms conservation and global implications.
Rice is a major cereal crop, negatively impacted by soil-salinity, both in terms of plant growth as well as productivity. Salinity tolerant rice varieties have been developed using conventional ...breeding approaches, however, there has been limited success which is primarily due to the complexity of the trait, low yield, variable salt stress response and availability of genetic resources. Furthermore, the narrow genetic base is a hindrance for further improvement of the rice varieties. Therefore, there is a greater need to screen available donor germplasm in rice for salinity tolerance related genes and traits. In this regard, genomics based techniques are useful for exploring new gene resources and QTLs. In rice, the vast allelic diversity existing in the wild and cultivated germplasm needs to be explored for improving salt tolerance. In the present review, we provide an overview of the allelic diversity in the Quantitative Trait Loci (QTLs) like Saltol, qGR6.2, qSE3 and RNC4 as well as genes like
,
(
) and
(salt tolerance level 1 gene) related to salt tolerance in rice. We have also discussed approaches for developing salt-tolerant cultivars by utilizing the effective QTLs or genes/alleles in rice.
Multi‐locus sequence data are widely used in fungal systematic and taxonomic studies to delimit species and infer evolutionary relationships. We developed and assessed the efficacy of a multi‐locus ...pooled sequencing method using PacBio long‐read high‐throughput sequencing. Samples included fresh and dried voucher specimens, cultures and archival DNA extracts of Agaricomycetes with an emphasis on the order Cantharellales. Of the 283 specimens sequenced, 93.6% successfully amplified at one or more loci with a mean of 3.3 loci amplified. Our method recovered multiple sequence variants representing alleles of rDNA loci and single copy protein‐coding genes rpb1, rpb2 and tef1. Within‐sample genetic variation differed by locus and taxonomic group, with the greatest genetic divergence observed among sequence variants of rpb2 and tef1 from corticioid Cantharellales. Our method is a cost‐effective approach for generating accurate multi‐locus sequence data coupled with recovery of alleles from polymorphic samples and multi‐organism specimens. These results have important implications for understanding intra‐individual genomic variation among genetic loci commonly used in species delimitation of fungi.
•Citrus halimii is not an interspecific hybrid but a true wild citrus species.•C. halimii shares a commune ancestor with kumquats (Fortunella sp.).•The essential oils of C. halimii present original ...compounds never described in citrus.•Germacrene d-8-one is specific to C. halimii representing 8.7% of total leaf essential oil.
Citrus phylogeny is currently based on genome analysis using molecular markers and sequencing. The 7 pure genetic groups that gave rise to all cultivated citrus underlie the diversity of citrus accessions originating from Asia. However, there are wild citrus forms whose phylogenetic position is unknown, such as mountain citron (Citrus halimii B.C. Stone) that was discovered in Malaysia in the early 1970s. We sought to elucidate its status by determining its genetic profile with 30 SSR and InDel markers distributed on the 9 chromosomes of the citrus reference genome as compared to those of the 7 pure genetic groups represented by 4 or 5 varieties each. The genetic study was supplemented by a comparison of the composition of essential oils obtained by fruit peel and leaf hydrodistillation to those of the citrus fruits used for genotyping. The genetic study demonstrated that C. halimii is not an interspecific hybrid (low heterozygosity) but rather a true species that shares a common ancestor with kumquats (Fortunella sp.), which would have evolved separately. The fruit aromatic profiles confirmed this kumquat/mountain citron relationship but also highlighted the uniqueness of C. halimii due to the presence of high proportions of compounds that have never been observed in other citrus fruits, such as germacrene d-8-one (accounting for 8.7% of the leaf essential oil).
Sugarcane (Saccharum) is the most critical sugar crop worldwide. As one of the most enriched transcription factor families in plants, MYB genes display a great potential to contribute to sugarcane ...improvement by trait modification. We have identified the sugarcane MYB gene family at a whole-genome level through systematic evolution analyses and expression profiling. R2R3-MYB is a large subfamily involved in many plant-specific processes. A total of 202 R2R3-MYB genes (356 alleles) were identified in the polyploid Saccharum spontaneum genomic sequence and classified into 15 subgroups by phylogenetic analysis. The sugarcane MYB family had more members by a comparative analysis in sorghum and significant advantages among most plants, especially grasses. Collinearity analysis revealed that 70% of the SsR2R3-MYB genes had experienced duplication events, logically suggesting the contributors to the MYB gene family expansion. Functional characterization was performed to identify 56 SsR2R3-MYB genes involved in various plant bioprocesses with expression profiling analysis on 60 RNA-seq databases. We identified 22 MYB genes specifically expressed in the stem, of which RT-qPCR validated MYB43, MYB53, MYB65, MYB78, and MYB99. Allelic expression dominance analysis implied the differential expression of alleles might be responsible for the high expression of MYB in the stem. MYB169, MYB181, MYB192 were identified as candidate C.sub.4 photosynthetic regulators by C.sub.4 expression pattern and robust circadian oscillations. Furthermore, stress expression analysis showed that MYB36, MYB48, MYB54, MYB61 actively responded to drought treatment; 19 and 10 MYB genes were involved in response to the sugarcane pokkah boeng and mosaic disease, respectively. This is the first report on genome-wide analysis of the MYB gene family in sugarcane. SsMYBs probably played an essential role in stem development and the adaptation of various stress conditions. The results will provide detailed insights and rich resources to understand the functional diversity of MYB transcription factors and facilitate the breeding of essential traits in sugarcane.
Allelic diversity of human leukocyte antigen (HLA) class II genes may help maintain humoral immunity against infectious diseases. In this study, we investigated germline genetic variation in ...classical HLA class II genes and employed a systematic, unbiased approach to explore the relative contribution of this genetic variation in the antibody repertoire to various common pathogens. We leveraged a well-defined cohort of 800 adults representing the general Arab population in which genetic material is shared because of the high frequency of consanguineous unions. By applying a high-throughput method for large-scale antibody profiling to this well-defined cohort, we were able to dissect the overall effect of zygosity for classical HLA class II genes, as well as the effects associated with specific HLA class II alleles, haplotypes and genotypes, on the antimicrobial antibody repertoire breadth and antibody specificity with unprecedented resolution. Our population genetic studies revealed that zygosity of the classical HLA class II genes is a strong predictor of antibody responses to common human pathogens, suggesting that classical HLA class II gene heterozygosity confers a selective advantage. Moreover, we demonstrated that multiple HLA class II alleles can have additive effects on the antibody repertoire to common pathogens. We also identified associations of HLA-DRB1 genotypes with specific antigens. Our findings suggest that HLA class II gene polymorphisms confer specific humoral immunity against common pathogens, which may have contributed to the genetic diversity of HLA class II loci during hominine evolution.
Pathogen‐mediated selection and sexual selection are important drivers of evolution. Both processes are known to target genes of the major histocompatibility complex (MHC), a gene family encoding ...cell‐surface proteins that display pathogen peptides to the immune system. The MHC is also a model for understanding processes such as gene duplication and trans‐species allele sharing. The class II MHC protein is a heterodimer whose peptide‐binding groove is encoded by an MHC‐IIA gene and an MHC‐IIB gene. However, our literature review found that class II MHC papers on infectious disease or sexual selection included IIA data only 18% and 9% of the time, respectively. To assess whether greater emphasis on MHC‐IIA is warranted, we analysed MHC‐IIA sequence data from 50 species of vertebrates (fish, amphibians, birds, mammals) to test for polymorphism and positive selection. We found that the number of MHC‐IIA alleles within a species was often high, and covaried with sample size and number of MHC‐IIA genes assayed. While MHC‐IIA variability tended to be lower than that of MHC‐IIB, the difference was only ~25%, with ~3 fewer IIA alleles than IIB. Furthermore, the unexpectedly high MHC‐IIA variability showed clear signatures of positive selection in most species, and positive selection on MHC‐IIA was stronger in fish than in other surveyed vertebrate groups. Our findings underscore that MHC‐IIA can be an important target of selection. Future studies should therefore expand the characterization of MHC‐IIA at both allelic and genomic scales, and incorporate MHC‐IIA into models of fitness consequences of MHC variation.
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