Summary
Though several genes governing various major traits have been reported in rice, their superior haplotype combinations for developing ideal variety remains elusive. In this study, haplotype ...analysis of 120 previously functionally characterized genes, influencing grain yield (87 genes) and grain quality (33 genes) revealed significant variations in the 3K rice genome (RG) panel. For selected genes, meta‐expression analysis using already available datasets along with co‐expression network provided insights at systems level. Also, we conducted candidate gene based association study for the 120 genes and identified 21 strongly associated genes governing 10‐grain yield and quality traits. We report superior haplotypes upon phenotyping the subset of 3K RG panel, SD1‐H8 with haplotype frequency (HF) of 30.13% in 3K RG panel, MOC1‐H9 (HF: 23.08%), IPA1‐H14 (HF: 6.64%), DEP3‐H2 (HF: 5.59%), DEP1‐H2 (HF: 37.53%), SP1‐H3 (HF: 5.05%), LAX1‐H5 (HF: 1.56%), LP‐H13 (3.64%), OSH1‐H4 (5.52%), PHD1‐H14 (HF: 15.21%), AGO7‐H15 (HF: 3.33%), ROC5‐H2 (31.42%), RSR1‐H8 (HF: 4.20%) and OsNAS3‐H2 (HF: 1.00%). For heading date, Ghd7‐H8 (HF: 3.08%), TOB1‐H10 (HF: 4.60%) flowered early, Ghd7‐H14 (HF: 42.60%), TRX1‐H9 (HF: 27.97%), OsVIL3‐H14 (HF: 1.72%) for medium duration flowering, while Ghd7‐H6 (HF: 1.65%), SNB‐H9 (HF: 9.35%) were late flowering. GS5‐H4 (HF: 65.84%) attributed slender, GS5‐H5 (HF: 29.00%), GW2‐H2 (HF: 4.13%) were medium slender and GS5‐H9 (HF: 2.15%) for bold grains. Furthermore, haplotype analysis explained possible genetic basis for superiority of selected mega‐varieties. Overall, this study suggests the possibility for developing next‐generation tailor‐made rice with superior haplotype combinations of target genes suiting future food and nutritional demands via haplotype‐based breeding.
The major histocompatibility complex (MHC) is a central component of the vertebrate immune system and hence evolves in the regime of a host–pathogen evolutionary race. The MHC is associated with ...quantitative traits which directly affect fitness and are subject to selection pressure. The evolution of haplotypes at the MHC HLA (HLA) locus is generally thought to be governed by selection for increased diversity that is manifested in overdominance and/or negative frequency-dependent selection (FDS). However, recently, a model combining purifying selection on haplotypes and balancing selection on alleles has been proposed. We compare the predictions of several population dynamics models of haplotype frequency evolution to the distributions derived from 6.59-million-donor HLA typings from the National Marrow Donor Program registry. We show that models that combine a multiplicative fitness function, extremely high haplotype discovery rates, and exponential fitness decay over time produce the best fit to the data for most of the analyzed populations. In contrast, overdominance is not supported, and population substructure does not explain the observed haplotype frequencies. Furthermore, there is no evidence of negative FDS. Thus, multiplicative fitness, rapid haplotype discovery, and rapid fitness decay appear to be the major factors shaping the HLA haplotype frequency distribution in the human population.
The first release of UK Biobank whole-genome sequence data contains 150,119 genomes. We present an open-source pipeline for filtering, phasing, and indexing these genomes on the cloud-based UK ...Biobank Research Analysis Platform. This pipeline makes it possible to apply haplotype-based methods to UK Biobank whole-genome sequence data. The pipeline uses BCFtools for marker filtering, Beagle for genotype phasing, and Tabix for VCF indexing. We used the pipeline to phase 406 million single-nucleotide variants on chromosomes 1–22 and X at a cost of £2,309. The maximum time required to process a chromosome was 2.6 days. In order to assess phase accuracy, we modified the pipeline to exclude trio parents. We observed a switch error rate of 0.0016 on chromosome 20 in the White British trio offspring. If we exclude markers with nonmajor allele frequency < 0.1% after phasing, this switch error rate decreases by 80% to 0.00032.
We present an open-source pipeline for filtering, phasing, and indexing 150,119 UK Biobank genomes. This pipeline makes it possible to apply haplotype-based methods to these data. We use the pipeline to phase 406 million single-nucleotide variants on chromosomes 1–22 and X at a cost of £2,309.
Common single-nucleotide polymorphisms (SNPs) are predicted to collectively explain 40-50% of phenotypic variation in human height, but identifying the specific variants and associated regions ...requires huge sample sizes
. Here, using data from a genome-wide association study of 5.4 million individuals of diverse ancestries, we show that 12,111 independent SNPs that are significantly associated with height account for nearly all of the common SNP-based heritability. These SNPs are clustered within 7,209 non-overlapping genomic segments with a mean size of around 90 kb, covering about 21% of the genome. The density of independent associations varies across the genome and the regions of increased density are enriched for biologically relevant genes. In out-of-sample estimation and prediction, the 12,111 SNPs (or all SNPs in the HapMap 3 panel
) account for 40% (45%) of phenotypic variance in populations of European ancestry but only around 10-20% (14-24%) in populations of other ancestries. Effect sizes, associated regions and gene prioritization are similar across ancestries, indicating that reduced prediction accuracy is likely to be explained by linkage disequilibrium and differences in allele frequency within associated regions. Finally, we show that the relevant biological pathways are detectable with smaller sample sizes than are needed to implicate causal genes and variants. Overall, this study provides a comprehensive map of specific genomic regions that contain the vast majority of common height-associated variants. Although this map is saturated for populations of European ancestry, further research is needed to achieve equivalent saturation in other ancestries.
Massive genotyping in cattle has uncovered several deleterious haplotypes that cause pre-term mortality. Holstein Haplotype 5 (HH5) is a deleterious haplotype present in the Holstein Friesian ...population that involves the ablation of the Transcription Factor B1 mitochondrial (TFB1M) gene. The developmental stage at which HH5 double-carrier (DC, homozygous) embryos or fetuses die remains unknown and this is a relevant information to estimate the economic losses associated to the inadvertent cross between carriers. To determine if HH5 DC survive to maternal recognition of pregnancy, embryonic day (E)14 embryos were flushed from superovulated carrier cows inseminated with a carrier bull. DC E14 conceptuses were recovered at Mendelian rates but they failed to achieve early elongation, as evidenced by a drastic (>26-fold) reduction in the proliferation of extraembryonic membranes compared with carrier or non-carrier embryos. To assess development at earlier stages, TFB1M knockout (KO) embryos -functionally equivalent to DC embryos- were generated by CRISPR technology and cultured to the blastocyst stage -Day (D)8- and to the early embryonic disc stage -D12-. No significant effect of TFB1M ablation was observed on the differentiation and proliferation of embryonic lineages and relative mtDNA content up to D12. In conclusion, HH5 DC embryos are able to develop to early embryonic disc stage but fail to undergo early conceptus elongation, required for pregnancy recognition.
Haplotype-based breeding (HBB) is one of the cutting-edge technologies in the realm of crop improvement due to the increasing availability of Single Nucleotide Polymorphisms identified by Next ...Generation Sequencing technologies. The complexity of the data can be decreased with fewer statistical tests and a lower probability of spurious associations by combining thousands of SNPs into a few hundred haplotype blocks. The presence of strong genomic regions in breeding lines of most crop species facilitates the use of haplotypes to improve the efficiency of genomic and marker-assisted selection. Haplotype-based breeding as a Genomic Assisted Breeding (GAB) approach harnesses the genome sequence data to pinpoint the allelic variation used to hasten the breeding cycle and circumvent the challenges associated with linkage drag. This review article demonstrates ways to identify candidate genes, superior haplotype identification, haplo-pheno analysis, and haplotype-based marker-assisted selection. The crop improvement strategies that utilize superior haplotypes will hasten the breeding progress to safeguard global food security.
•Haplotype-based breeding unlock the genetic variations in genetic resources for the crop improvement.•Haplotype-based breeding in rice based on the genome sequence data available and they are resequenced further for identification of haplotypes.•It is expected to integrate with biotechnological tools such as precise genome editing, functional genomics to facilitate the acceleration of genetic gain and to address global food security.
Bats (order, Chiroptera) account for more than one-fifth of all mammalian species in the world and are infected by various intra-erythrocytic parasites of the family Plasmodiidae (Apicomplexa: ...Haemosporida), including
Polychromophilus
Dionisi, 1899. Recent advance in the molecular characterization of haemosporidian isolates has enabled their accurate identification, particularly in the last decade. Studies are actively conducted in tropical regions, Europe, and Australia; however, data on haemosporidian infection in bats in Asian temperate areas, including Japan, remain limited. In this study, 75 bats of 4 species (
Miniopterus fuliginosus
,
Myotis macrodactylus
,
Rhinolophus nippon
, and
Rhinolophus cornutus
) were captured at three sites in western Japan (Yamaguchi Prefecture), and haemosporidian parasites were screened microscopically and molecularly via nested polymerase chain reaction (PCR) targeting the cytochrome
b
(
cytb
), cytochrome
c
oxidase subunit I (
cox-1
), apicoplast caseinolytic protease C (
clpc
), and nuclear elongation factor 2 (EF2) genes. The survey detected
Polychromophilus melanipherus
in 15 (40.5%) miniopterid bats (
M. fuliginosus
) and
Polychromophilus murinus
in 6 (46.2%) vespertilionid bats (
M. macrodactylus
), whereas none of the 25 rhinolophid bats (
R. nippon
and
R. cornutus
) was infected, indicating the robust host specificity for miniopterid (
P. melanipherus
) and vespertilionid (
P. murinus
) bats regardless of orthotopic nesting. The 15
Polychromophilus cytb
sequences obtained from 11 miniopterid and 4 vespertilionid bats were classified into six
cytb
haplotypes (three for each species), showing no region-specific variation in a phylogenetic tree of
Polychromophilus
isolates in the Old World. Similarly, multiple haplotypes (seven for
cox-1
and nine for
clpc
) and genotypes (three for EF2) were characterized for the Japanese isolates of
Polychromophilus
, and the results were consistent with those based on a haemosporidian
cytb
analysis. Bat flies (
Nycteribia allotopa
and another undetermined
Nycteribia
sp.) collected from the body surface of bats harbored
Polychromophilus
oocysts on the external surface of the midgut. This is the first study to report the isolation and molecular characterization of
Polychromophilus
spp. in miniopterid and vespertilionid bats in the temperate area of Asia (western Japan). Future studies should evaluate the global prevalence of haemosporidian infections in bats.
Plant landraces represent heterogeneous, local adaptations of domesticated species, and thereby provide genetic resources that meet current and new challenges for farming in stressful environments. ...These local ecotypes can show variable phenology and low-to-moderate edible yield, but are often highly nutritious. The main contributions of landraces to plant breeding have been traits for more efficient nutrient uptake and utilization, as well as useful genes for adaptation to stressful environments such as water stress, salinity, and high temperatures. We propose that a systematic landrace evaluation may define patterns of diversity, which will facilitate identifying alleles for enhancing yield and abiotic stress adaptation, thus raising the productivity and stability of staple crops in vulnerable environments.
Global climate change emphasizes the need to use better-adapted cultivars of the main crops and landraces as potential donors of useful genes.
The contribution of modern agriculture to total human-made greenhouse gas emissions is approximately 30%, and a shift to agro-ecological modes of production is increasingly seen as urgent, with landraces playing an important role in breeding programs.
During the past few decades interest in landrace conservation has been growing, with much research focusing on the maintenance of on-farm crop genetic diversity.
There is increasing consumer concern worldwide about food safety and nutrition. Landraces or old crop cultivars may provide solutions as sources of healthy and nutritious food.
This study describes the use of the 27 loci Yfiler® Plus kit and TaqMan™ SNP genotyping to characterise and predict the haplogroups of Y chromosomes within the four major ethnic populations of Ghana. ...Haplogroups were assigned using the desktop NevGen software (https://www.nevgen.org/). The E1b1a and E1b1b haplogroups are the most common in the Ghanaian population and form 95% of the dataset. The Mole-Dagomba sub-population had 4. 8% assigned to the haplogroups G, H, R1b, R2 and T. The Ewe had two samples assigned to haplogroups C and D whilst the Akan had one sample each assigned to haplogroups B, J1 and J2. The NevGen predicted haplogroups were further screened with TaqMan™ genotyping for confirmation. In conclusion, ≈ 95% of the dataset was classified as M-E1b1a using NevGen combined with TaqMan™ SNP Genotyping for confirmation. The TaqMan™ also revealed 5% as J1 and other haplogroups, using an in-house control from the J1 haplogroup.
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