Genomic Reference Resource for African Cattle: Genome Sequences and High-Density Array Variants

As African indigenous cattle evolved in a hot tropical climate, they have developed an inherent thermotolerance; survival mechanisms include a light-colored and shiny coat, increased sweating, and cellular and molecular mechanisms to cope with high environmental temperature. Here, we report the positive selection signature of genes in African cattle breeds which contribute for their heat tolerance mechanisms. We compared the genomes of five indigenous African cattle breeds with the genomes of four commercial cattle breeds using cross-population composite likelihood ratio (XP-CLR) and cross-population extended haplotype homozygosity (XP-EHH) statistical methods. We identified 296 (XP-EHH) and 327 (XP-CLR) positively selected genes. Gene ontology analysis resulted in 41 biological process terms and six Kyoto Encyclopedia of Genes and Genomes pathways. Several genes and pathways were found to be involved in oxidative stress response, osmotic stress response, heat shock response, hair and skin properties, sweat gland development and sweating, feed intake and metabolism, and reproduction functions. The genes and pathways identified directly or indirectly contribute to the superior heat tolerance mechanisms in African cattle populations. The result will improve our understanding of the biological mechanisms of heat tolerance in African cattle breeds and opens an avenue for further study.

Genomic research in any organism encompasses understanding structure of the target genome and genes, their function, and evolution. Brassica rapa, which is phylogenetically related to Arabidopsis thaliana, is an important species with respect to its uses as vegetable, oil, and fodder. The availability of suitable genetic and genomic resources is a prerequisite to undertake genomic research in B. rapa. We have developed reference mapping populations of Chinese cabbage (B. rapa ssp. pekinensis) comprising 78 doubled haploid lines and over 250 recombinant inbred lines. Two Bacterial Artificial Chromosome (BAC) libraries, generated by restriction enzymes HindIII (KBrH) and BamHI (KBrB), comprise 56 592 and 50 688 clones, respectively. We have also constructed 22 cDNA libraries from different plant tissues consisting of 104 914 clones with an average length of 575 bp. Initial BAC‐end sequence analysis of 1473 clones of the KBrH library led us to understand the structure of B. rapa genome with respect to extent of genic sequences and their annotation, and relative abundance of different types of repetitive DNAs. Full‐length sequence analysis of BAC clones revealed extensive triplication of B. rapa DNA segments coupled with variable gene losses within the segments. The formulation of the ‘Multinational Brassica Genome Project’ has laid the foundation to sequence the complete genome of B. rapa ssp. pekinensis by the international Brassica research community. It has been proposed to undertake BAC‐to‐BAC sequencing of genetically mapped seed BACs. In recent years, development of bioinformatics tools in Brassica has given a boost to structural genomics research in Brassica species. The research undertaken with the availability of various genomic resources in the public domain has added to our understanding of the structure of B. rapa.

Saccharomyces cerevisiae (baker's yeast, budding yeast) is one of the most important model organisms for biological research and is a crucial microorganism in industry. Currently, a huge number of Saccharomyces cerevisiae genome sequences are available at the public domain. However, these genomes are distributed at different websites and a large number of them are released without annotation information. To provide one complete annotated genome data resource, we collected 2,507 Saccharomyces cerevisiae genome assemblies and re-annotated 2,506 assemblies using a custom annotation pipeline, producing a total of 15,407,164 protein-coding gene models. With a custom pipeline, all these gene sequences were clustered into families. A total of 1,506 single-copy genes were selected as marker genes, which were then used to evaluate the genome completeness and base qualities of all assemblies. Pangenomic analyses were performed based on a selected subset of 847 medium-high-quality genomes. Statistical comparisons revealed a number of gene families showing copy number variations among different organism sources. To the authors' knowledge, this study represents the largest genome annotation project of S. cerevisiae so far, providing rich genomic resources for the future studies of the model organism S. cerevisiae and its relatives.IMPORTANCESaccharomyces cerevisiae (baker's yeast, budding yeast) is one of the most important model organisms for biological research and is a crucial microorganism in industry. Though a huge number of Saccharomyces cerevisiae genome sequences are available at the public domain, these genomes are distributed at different websites and most are released without annotation, hindering the efficient reuse of these genome resources. Here, we collected 2,507 genomes for Saccharomyces cerevisiae, performed genome annotation, and evaluated the genome qualities. All the obtained data have been deposited at public repositories and are freely accessible to the community. This study represents the largest genome annotation project of S. cerevisiae so far, providing one complete annotated genome data set for S. cerevisiae, an important workhorse for fundamental biology, biotechnology, and industry.

Knowledge of the extent of linkage disequilibrium (LD) between markers is crucial for determining the number of markers required for quantitative trait loci mapping, genome-wide association studies, and application of marker-assisted selection. In this study, we surveyed genome-wide LD using three genotyping BeadChips (9, 50, and 80 K) in 11 indigenous Ethiopian cattle populations and the Korean (Hanwoo) cattle breed. The overall mean r 2 values were 0.05 ± 0.12, 0.12 ± 0.20, and 0.20 ± 0.24 in the Ethiopian cattle populations for the 9, 50, and 80 K genotyping BeadChips, respectively. In Hanwoo cattle, these values were respectively 0.06 ± 0.13, 0.15 ± 0.23, and 0.15 ± 0.26. The level of LD was significantly affected by breed, genotyping BeadChip, and chromosome (P < 0.0001). For Ethiopian cattle populations, a moderate level of LD (r 2 = 0.22) extended at marker distances of 20–40 kb for the indicine-derived 80 K BeadChip, whereas it was only 0.14 for the 50 K BeadChip. As a consequence of the moderate r 2 , genome-wide association studies in Ethiopian cattle populations require 75,000–150,000 indicine-derived SNPs (with a MAF ≥ 0.05). We suggest that indicine-derived SNPs maybe more suitable for genome-wide association studies and genomic selection in indigenous Ethiopian (or African) cattle populations.

Cowpea ( Vigna unguiculata (L.) Walp) is an important legume crop for food security in areas of low-input and smallholder farming throughout Africa and Asia. Genetic improvements are required to increase yield and resilience to biotic and abiotic stress and to enhance cowpea crop performance. An integrated cowpea genomic and gene expression data resource has the potential to greatly accelerate breeding and the delivery of novel genetic traits for cowpea. Extensive genomic resources for cowpea have been absent from the public domain; however, a recent early release reference genome for IT97K-499-35 ( Vigna unguiculatav1.0, NSF, UCR, USAID, DOE-JGI, http://phytozome.jgi.doe.gov/) has now been established in a collaboration between the Joint Genome Institute (JGI) and University California (UC) Riverside. Here we release supporting genomic and transcriptomic data for two transformable cowpea varieties, IT97K-499-35 and IT86D-1010. The transcriptome resource includes six tissue-specific datasets for each variety, with particular emphasis on reproductive tissues that extend and support the V. unguiculata v1.0 reference. Annotations have been included in our resource to allow direct mapping to the v1.0 cowpea reference. The resource described here is supported by downloadable raw and assembled sequence data.

BackgroundPigeonpea (Cajanus cajan (L.) Millsp) is one of the major grain legume crops of the tropics and subtropics, but biotic stresses [Fusarium wilt (FW), sterility mosaic disease (SMD), etc.] are serious challenges for sustainable crop production. Modern genomic tools such as molecular markers and candidate genes associated with resistance to these stresses offer the possibility of facilitating pigeonpea breeding for improving biotic stress resistance. Availability of limited genomic resources, however, is a serious bottleneck to undertake molecular breeding in pigeonpea to develop superior genotypes with enhanced resistance to above mentioned biotic stresses. With an objective of enhancing genomic resources in pigeonpea, this study reports generation and analysis of comprehensive resource of FW- and SMD- responsive expressed sequence tags (ESTs).ResultsA total of 16 cDNA libraries were constructed from four pigeonpea genotypes that are resistant and susceptible to FW ('ICPL 20102' and 'ICP 2376') and SMD ('ICP 7035' and 'TTB 7') and a total of 9,888 (9,468 high quality) ESTs were generated and deposited in dbEST of GenBank under accession numbers GR463974 to GR473857 and GR958228 to GR958231. Clustering and assembly analyses of these ESTs resulted into 4,557 unique sequences (unigenes) including 697 contigs and 3,860 singletons. BLASTN analysis of 4,557 unigenes showed a significant identity with ESTs of different legumes (23.2-60.3%), rice (28.3%), Arabidopsis (33.7%) and poplar (35.4%). As expected, pigeonpea ESTs are more closely related to soybean (60.3%) and cowpea ESTs (43.6%) than other plant ESTs. Similarly, BLASTX similarity results showed that only 1,603 (35.1%) out of 4,557 total unigenes correspond to known proteins in the UniProt database (≤ 1E-08). Functional categorization of the annotated unigenes sequences showed that 153 (3.3%) genes were assigned to cellular component category, 132 (2.8%) to biological process, and 132 (2.8%) in molecular function. Further, 19 genes were identified differentially expressed between FW- responsive genotypes and 20 between SMD- responsive genotypes. Generated ESTs were compiled together with 908 ESTs available in public domain, at the time of analysis, and a set of 5,085 unigenes were defined that were used for identification of molecular markers in pigeonpea. For instance, 3,583 simple sequence repeat (SSR) motifs were identified in 1,365 unigenes and 383 primer pairs were designed. Assessment of a set of 84 primer pairs on 40 elite pigeonpea lines showed polymorphism with 15 (28.8%) markers with an average of four alleles per marker and an average polymorphic information content (PIC) value of 0.40. Similarly, in silico mining of 133 contigs with ≥ 5 sequences detected 102 single nucleotide polymorphisms (SNPs) in 37 contigs. As an example, a set of 10 contigs were used for confirming in silico predicted SNPs in a set of four genotypes using wet lab experiments. Occurrence of SNPs were confirmed for all the 6 contigs for which scorable and sequenceable amplicons were generated. PCR amplicons were not obtained in case of 4 contigs. Recognition sites for restriction enzymes were identified for 102 SNPs in 37 contigs that indicates possibility of assaying SNPs in 37 genes using cleaved amplified polymorphic sequences (CAPS) assay.ConclusionThe pigeonpea EST dataset generated here provides a transcriptomic resource for gene discovery and development of functional markers associated with biotic stress resistance. Sequence analyses of this dataset have showed conservation of a considerable number of pigeonpea transcripts across legume and model plant species analysed as well as some putative pigeonpea specific genes. Validation of identified biotic stress responsive genes should provide candidate genes for allele mining as well as candidate markers for molecular breeding.

Genome resource banking of biomedically important laboratory animals

Understanding the nature of linkage disequilibrium (LD) between molecular markers reflects the degree of non-random association between their alleles, which is essential for genome-wide association studies. The main objective of this study was to assess the chromosome-wise linkage disequilibrium and haplotype block structure in indigenous cattle breeds of Tamil Nadu, India. A total of 79 animals belonging to five indigenous cattle breeds were considered as single indigenous cattle population and three samples per breed were sequenced using Illumina NovaSeqTM 6000 and Illumina HiSeq 2500. The LD parameter (r2) was estimated for a total of 62,095,778 pair- wise SNPs for all autosomes. The chromosome-wise number of SNP pairs, mean r2±standard deviation and median r2 values were 2,141,234, 0.484±0.246 and 0.493, respectively. Chromosome-wise mean r2 of different distance bins were calculated and it showed the maximum r2 value of 0.839 at 31-70 kb distance for Chromosome 11 and minimum r2 value of zero for Chromosome 7, 11, 15, 20 and 29, respectively at a distance 71-100 kb. This study also revealed a total of 413, 277 haplotype blocks which covered 2.34% of the autosomal genome. There was a total of 1,589,118 SNPs distributed within the haplotype blocks, covering a total length of 53.62 mb. The results of the study suggest the need for breed-specific reference populations for indigenous cattle breeds, which have a greater density of molecular markers of economic significance and thereby to identify breed-specific haplotypes in future.

Conventional pre-genomics breeding methodologies have significantly improved crop yields since the mid-twentieth century. Genomics provides breeders with advanced tools for whole-genome study, enabling a direct genotype–phenotype analysis. This shift has led to precise and efficient crop development through genomics-based approaches, including molecular markers, genomic selection, and genome editing. Molecular markers, such as SNPs, are crucial for identifying genomic regions linked to important traits, enhancing breeding accuracy and efficiency. Genomic resources viz. genetic markers, reference genomes, sequence and protein databases, transcriptomes, and gene expression profiles, are vital in plant breeding and aid in the identification of key traits, understanding genetic diversity, assist in genomic mapping, support marker-assisted selection and speeding up breeding programs. Advanced techniques like CRISPR/Cas9 allow precise gene modification, accelerating breeding processes. Key techniques like Genome-Wide Association study (GWAS), Marker-Assisted Selection (MAS), and Genomic Selection (GS) enable precise trait selection and prediction of breeding outcomes, improving crop yield, disease resistance, and stress tolerance. These tools are handy for complex traits influenced by multiple genes and environmental factors. This paper explores new genomic technologies like molecular markers, genomic selection, and genome editing for plant breeding showcasing their impact on developing new plant varieties.

BackgroundThe increasing demand for wood owing to societal development has highlighted the potential of Albizia odoratissima, a valuable timber species, to address significant timber shortages in China. However, the lack of effective genetic and genomic resources has limited the development and utilization of this species.ResultsIn this study, we utilised 95.3 Gb of HiFi reads to assemble a draft genome of A. odoratissima, resulting in a genome size of 788 Mb, comprising 511 contigs. We conducted whole-genome resequencing on 106 individuals from 7 populations on Hainan Island to explore these resources. Our analysis identified 498,308 high-quality single nucleotide polymorphisms, which were used to assess the genetic diversity, structure, and demographic history of A. odoratissima on Hainan Island. The results indicated that the genetic diversity of A. odoratissima on Hainan Island is relatively low (observed heterozygosity = 0.189, expected heterozygosity = 0.189, genetic diversity = 1.319 × 10−4) with minimal genetic differentiation (Fst = 0.0151) among the seven populations. Furthermore, molecular variance, principal coordinate analysis, neighbour-joining tree analysis, and genetic structure analysis revealed a shallow population structure. The linkage disequilibrium (LD) decay ranged from 11.4 kb for Jianfengling (JFL) to 39.2 kb for Wuzhishan (WZS). LD decay, demographic history, and Tajima’s D analyses indicated that the WZS population has experienced a bottleneck effect.ConclusionsThis study offers new insights into the genetic diversity and population structure of A. odoratissima on Hainan Island, providing a foundation for future resource utilization and genetic improvement strategies for this species.

Breeding indigenous African taurine cattle tolerant to trypanosomosis is a straightforward approach to control costs generated by this disease. A recent study identified quantitative trait loci (QTL) underlying trypanotolerance traits in experimental crosses between tolerant N'Dama and susceptible Boran zebu cattle. As trypanotolerance is thought to result from local adaptation of indigenous cattle breeds, we propose an alternative and complementary approach to study the genetic architecture of this trait, based on the identification of selection signatures within QTL or candidate genes. A panel of 92 microsatellite markers was genotyped on 509 cattle belonging to four West African trypanotolerant taurine breeds and 10 trypanosusceptible European or African cattle breeds. Some of these markers were located within previously identified QTL regions or candidate genes, while others were chosen in regions assumed to be neutral. A detailed analysis of the genetic structure of these different breeds was carried out to confirm a priori grouping of populations based on previous data. Tests based on the comparison of the observed heterozygosities and variances in microsatellite allelic size among trypanotolerant and trypanosusceptible breeds led to the identification of two significantly less variable microsatellite markers. BM4440, one of these two outlier loci, is located within the confidence interval of a previously described QTL underlying a trypanotolerance-related trait. Detection of selection signatures appears to be a straightforward approach for unravelling the molecular determinism of trypanosomosis pathogenesis. We expect that a whole genome approach will help confirm these results and achieve a higher resolving power.

Genomic selection has proven effective for accelerating genetic improvement in livestock, but its application in developing countries faces challenges, particularly for numerically small breeds, wherein, establishing large, single-breed reference population is difficult. To address this limitation, current study aimed to investigate the effectiveness of multi-breed reference populations to improve the genomic prediction accuracy in numerically small breeds with limited phenotypic and genomic resources. Genotypic and phenotypic data from 1,298 Gir, 1,291 Sahiwal, and 500 Kankrej indigenous cattle were used to enhance the genomic prediction accuracy in Kankrej, utilizing a multi-breed reference population. Principal Component Analysis (PCA)-K-means-based clustering showed overlap between Gir and Kankrej, indicating genetic similarity between these two breeds. Linkage disequilibrium (LD) decay patterns corroborated these results, showing a similar trend in the LD decay plot in the Gir–Kankrej, suggesting shared haplotype blocks that can be utilized in combined analyses. Heritability estimates for 305-day first lactation milk yield (305-DMY) were 0.30 ± 0.07 for Gir, 0.27 ± 0.07 for Sahiwal, and 0.17 ± 0.01 for Kankrej cattle. Genomic estimated breeding values (GEBV) with single-breed reference population were predicted with accuracies of 0.65 for Gir, 0.60 for Sahiwal, and 0.49 for Kankrej. Multi-breed reference populations were created for all possible breed combinations. Three genomic evaluation strategies, viz., shared Genomic Relationship Matrix (GRM), non-shared GRM, and metafounder-corrected shared GRM, were compared. We observed a significant gain in accuracy for the numerically small breed, Kankrej, using a multi-breed approach as compared to a single-breed approach. Using a multi-breed evaluation with shared and non-shared GRM and the metafounder approach led to accuracy improvements of 23.6%, 24.6%, and 16.9%, respectively, while using the Gir-Kankrej multi-breed reference population. Validation using the linear regression (LR) method showed that the best way to predict GEBV for the Kankrej breed was through multi-breed evaluation with the ‘shared GRM’ approach. Our findings indicate that in the absence of large breed specific reference, multibreed genomic evaluation offers a viable strategy for enhancing genomic prediction accuracy for numerically small breeds in India.

BackgroundThe Pompeii worm Alvinella pompejana, a terebellid annelid, has long been an exemplar of a metazoan that lives in an extreme environment, on the chimney wall of deep-sea hydrothermal vents, but this very environment has made it difficult to study. Comprehensive assessment of Alvinella pompejana genome content, and the factors that could explain its ability to thrive in seemingly hostile conditions has been lacking.ResultsWe report the chromosome-level genome sequence of Alvinella pompejana and population-level sequence variants. We produced a set of gene models and analysed the predicted protein set in the light of past hypotheses about the thermotolerance of Alvinella, comparing it to other recently sequenced vent annelids. Despite its extreme environment, we find evidence for relatively conservative evolution of protein amino acid composition and genome evolution as measured by synteny. We suggest that prior hypotheses of loss of amino acid biosynthesis genes associated with obligate symbioses reported in siboglinid annelids are mistaken, and that Alvinella and siboglinids are typical metazoans in this regard. Alvinella encodes a number of respiratory enzymes unusual for bilaterian animals, suggesting an ability to better tolerate hypoxic environments. We find evidence of a parallel increase in the number of globin encoding genes and loss of light sensitive opsins and cryptochromes in deep-sea annelids.ConclusionsOur results provide a comprehensive Alvinella protein and genome resource and shed light on the adaptation of Alvinella to temperature, hypoxia and darkness, as well as cryptic speciation, giving a firm base from which future studies can be taken forward.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12915-025-02369-7.

Low-light (LL) stress caused by persistent cloud cover during the Kharif season significantly reduces rice (Oryza sativa L.) grain yield (GY) by limiting photosynthesis, impairing assimilate production, and affecting reproductive development. To dissect the genetic basis of LL tolerance, 192 diverse rice genotypes were evaluated across contrasting light environments (LL and normal light under Rabi and Kharif seasons) and genotyped using a high-density 44K single nucleotide polymorphism array. Integrating phenotypic and genomic data enabled a multi-tiered analysis from quantitative trait locus (QTL) discovery to gene identification and haplotype dissection. Genome-wide association analysis identified 305 QTLs associated with GY and 11 related traits, including 148 LL-specific and 32 stable QTLs expressed across both seasons. Forty-two candidate genes were localized within major QTL intervals, and 12 were identified as hub genes based on their key roles in photosynthesis, light perception, hormone signaling, and starch biosynthesis. These included Gn1a, OsPsbS1, OsAGPL2, OsLhcb1, OsAUX1, OsSBDCP1, OsNPF5.16, OsPHYA, OsPHYB, OsGIF1, HY5, and OsYUC11. Expression profiling confirmed stronger induction of OsPHYA (∼2.5-fold) and OsPsbS1 (∼2.8-fold) in LL-tolerant genotypes like Purnendu and Swarnaprabha compared to susceptible lines. Haplotype analysis revealed several superior alleles, such as PHYA-Hap2 and OsPsbS1-Hap3, that were consistently associated with higher spikelet fertility, greater grain number, increased biomass, and improved GY under LL, with top-performing haplotypes enhancing yield by 12%-18%. Genotypes carrying these haplotypes (e.g., Purnendu, Swarnaprabha, and Chamarmani) represent valuable breeding donors. Overall, this study provides the first genome-wide identification of LL-specific haplotypes in rice, together with biologically validated hub genes. These findings offer actionable genomic targets and donor resources for developing LL-resilient, high-yielding cultivars suited to changing climate and light-limited environments.

Levels of genetic differentiation, gene flow, and genetic structure of three indigenous cattle populations (Luxi, Bohai, and Minnan) and two reference cattle populations (Chinese Holstein and Qinhai yak) in China were estimated using the information from 12 microsatellites, and 141 microsatellite alleles were identified. The mean number of alleles per locus ranged from 2.9005 in yak to 4.9722 in Holstein. The observed heterozygosity ranged from 0.5325 (yak) to 0.7719 (Holstein); 29 private alleles were detected. The global heterozygote deficit across all populations amounted to 58.5% (p < 0.001). The overall significant (p < 0.001) deficit of heterozygotes because of inbreeding within breeds amounted to 43.2%. The five cattle populations were highly differentiated (F (st) = 26.9%, p < 0.001) at all loci. The heterozygote deficit within the population was highest in Luxi cattle and lowest in yak. The average number of effective migrants exchanged per generation was highest (1.149) between Luxi and Holstein, and lowest (0.509) between Luxi and yak. With the application of prior population information, cluster analysis achieved posterior probabilities from 91% to 98% of correctly assigning individuals to populations. Combining the information of cluster analysis, gene flow, and Structure analysis, the five cattle populations belong to three genetic clusters, a taurine (Luxi and Chinese Holstein), a zebu (Bohai and Minnan), and a yak cluster. This indicates that Bohai black is closer to Bos indicus than Luxi cattle. The evolution and development of three indigenous cattle populations are discussed.