Integrated GWAS and transcriptome analysis reveals key genes associated with muscle fibre and fat traits in Gushi chicken.

1. In the following experiment meat quality traits of a Gushi-Anka F2 resource population were measured, and their heritability estimated. Intramuscular fat (IMF) had medium heritability (0.35) but leg muscle fibre density (LMD), leg muscle fibre diameter (LMF), breast muscle fibre density (BMD), fresh fat content (FFA), and absolute dry fat content (AFC) had low heritability (0-0.2). The IMF presented the most important genetic additive effect among the poultry meat quality-related traits studied.2. The phenotypic data of meat quality traits in the Gushi-Anka F2 resource population were combined with genotyping by sequencing (GBS) data to obtain genotype data. Six meat quality traits in 734 birds were analysed by GWAS. Based on these variants, 83 significant (-log10(p) > 4.42) single nucleotide polymorphisms and four quantitative trait loci (QTL) regions corresponding to 175 genes were identified. Further linkage disequilibrium (LD) analysis was conducted on chromosome 13 (Chr13) and chromosome 27 (Chr27) QTL regions.3. Based on the transcriptome data and GWAS results, 12 shared genes - ITGB3, DNAJC27, ETV4, C7orf50, FKBP1B, G3BP1, IGF2BP1, KCNH6, LOC416263, SCARA5, SMIM5 and TBL1XR1 were identified as candidate genes influencing muscle fibre and fat traits.

Novel pathways linked to the expression of temperament in Merino sheep: a genome-wide association study.

Animal temperament refers to the inherent behavioural and emotional characteristics of an animal, influencing how it interacts with its environment. The selection of sheep for temperament can change the temperament traits of the selected line and improve the welfare and production (reproduction, growth, immunity) of those animals. To understand the genetics that underly variation in temperament in sheep, and how selection on temperament can affect other production traits, a genome-wide association study was carried out. Merino sheep from lines selected for traits of calm and nervous temperament, and a commercial population, on which the temperament traits had never been assessed, were used. Blood samples from the three populations were genotyped using an Illumina GGP Ovine 50 K Genotyping BeadChip. The calm and nervous populations in the selected lines presented as distinct genetic populations, and 2 729 of the 45 761 single nucleotide polymorphisms (SNPs) had significantly different proportions between the two lines. Of those 2 729 SNPs, 2 084 were also associated with temperament traits in the commercial population. A genomic annotation identified 81 candidate genes for temperament, nearly half of which are associated with disorders of social behaviour in humans. Five of those 81 candidate genes are related to production traits in sheep. Two genes were associated with personality disorders in humans and with production traits in sheep. We identified significant enrichment in genes involved in nervous system processes such as the regulation of systemic arterial blood pressure, ventricular myocyte action, multicellular organismal signalling, ion transmembrane transport, and calcium ion binding, suggesting that temperament is underpinned by variation in multiple biological systems. Our results contribute to understanding of the genetic basis of animal temperament which could be applied to the genetic evaluation of temperament in sheep and other farm animals.

Association mapping identifies stable loci containing novel genes for developmental and reproductive traits in sorghum.

Key message We mapped 11 sorghum traits, identified 33 candidate genes, and found a grain yield gene (GID1) that regulates seed development and a grass-specific tillering gene (DUF1618) transferred to Striga hermonthica.

Mining of Oil Content Genes in Recombinant Maize Inbred Lines with Introgression from Temperate and Tropical Germplasm.

The oil content of maize kernels is essential to determine its nutritional and economic value. A multiparent population (MPP) consisting of five recombinant inbred line (RIL) subpopulations was developed to elucidate the genetic basis of the total oil content (TOC) in maize. The MPP used the subtropical maize inbred lines CML312 and CML384, along with the tropical maize inbred lines CML395, YML46, and YML32 as the female parents, and Ye107 as the male parent. A genome-wide association study (GWAS) was performed using 429 RILs of the multiparent population across three environments, employing 584,847 high-quality single nucleotide polymorphisms (SNPs). Furthermore, linkage analysis was performed in the five subpopulations to identify quantitative trait loci (QTL) linked to TOC in maize. Through QTL mapping and GWAS, 18 QTLs and 60 SNPs that were significantly associated with TOC were identified. Two novel candidate genes, Zm00001d029550 and Zm00001d029551, related to TOC in maize and located on chromosome 1 were reported, which have not been previously reported. These genes are involved in biosynthesis, lipid signal transduction, plant development and metabolism, and stress responses, potentially influencing maize TOC. Haplotype analysis of Zm00001d029550 and Zm00001d029551 revealed that Hap3 could be considered a superior haplotype for increasing TOC in maize. A co-located SNP (SNP-75791466) on chromosome 1, located 5648 bp and 11,951 bp downstream of the candidate genes Zm00001d029550 and Zm00001d029551, respectively, was found to be expressed in various maize tissues. The highest expression was observed in embryos after pollination, indicating that embryos are the main tissue for oil accumulation in maize. This study provides a theoretical basis for understanding the genetic mechanisms underlying maize TOC and developing high-quality, high-oil maize varieties.

RNA-Seq Analysis and Candidate Gene Mining of Gossypium hirsutum Stressed by Verticillium dahliae Cultured at Different Temperatures.

The occurrence and spread of Verticillium dahliae (V. dahliae) in cotton depends on the combined effects of pathogens, host plants, and the environment, among which temperature is one of the most important environmental factors. Studying how temperature impacts the occurrence of V. dahliae in cotton and the mechanisms governing host defense responses is crucial for disease prevention and control. Understanding the dual effects of temperature on both pathogens and hosts can provide valuable insights for developing effective strategies to manage this destructive fungal infection in cotton. This study was based on the deciduous V. dahliae Vd-3. Through cultivation at different temperatures, Vd-3 formed the most microsclerotia and had the largest colony diameter at 25 °C. Endospore toxins were extracted, and 48 h was determined to be the best pathogenic time point for endotoxins to infect cotton leaves through a chlorophyll fluorescence imaging system and phenotypic evaluation. Transcriptome sequencing was performed on cotton leaves infected with Vd-3 endotoxins for 48 h at different culture temperatures. A total of 34,955 differentially expressed genes (DEGs) were identified between each temperature and CK (no pathogen inoculation), including 17,422 common DEGs. The results of the enrichment analysis revealed that all the DEGs were involved mainly in photosynthesis and sugar metabolism. Among the 34,955 DEGs, genes in the biosynthesis and signal transduction pathways of jasmonic acid (JA), salicylic acid (SA), and ethylene (ET) were identified, and their expression patterns were determined. A total of 5652 unique DEGs were clustered into six clusters using the k-means clustering algorithm, and the functions and main transcription factors (TFs) of each cluster were subsequently annotated. In addition, we constructed a gene regulatory network via weighted correlation network analysis (WGCNA) and identified twelve key genes related to cotton defense against V. dahliae at different temperatures, including four genes encoding transcription factors. These findings provide a theoretical foundation for investigating temperature regulation in V. dahliae infecting cotton and introduce novel genetic resources for enhancing resistance to this disease in cotton plants.

GWAS and Meta-QTL Analysis of Kernel Quality-Related Traits in Maize.

The quality of corn kernels is crucial for their nutritional value, making the enhancement of kernel quality a primary objective of contemporary corn breeding efforts. This study utilized 260 corn inbred lines as research materials and assessed three traits associated with grain quality. A genome-wide association study (GWAS) was conducted using the best linear unbiased estimator (BLUE) for quality traits, resulting in the identification of 23 significant single nucleotide polymorphisms (SNPs). Additionally, nine genes associated with grain quality traits were identified through gene function annotation and prediction. Furthermore, a total of 697 quantitative trait loci (QTL) related to quality traits were compiled from 27 documents, followed by a meta-QTL analysis that revealed 40 meta-QTL associated with these traits. Among these, 19 functional genes and reported candidate genes related to quality traits were detected. Three significant SNPs identified by GWAS were located within the intervals of these QTL, while the remaining eight significant SNPs were situated within 2 Mb of the QTL. In summary, the findings of this study provide a theoretical framework for analyzing the genetic basis of corn grain quality-related traits and for enhancing corn quality.

Genome-Wide Association Study of Reproductive Traits in Large White Pigs.

(1) Background: Reproductive performance is crucial for the pork industry's success. The Large White pig is central to this, yet the genetic factors influencing its reproductive traits are not well understood, highlighting the need for further research. (2) Methods: This study utilized Genome-Wide Association Studies to explore the genetic basis of reproductive traits in the Large White pig. We collected data from 2237 Large White sows across four breeding herds in southern China, focusing on eight reproductive traits. Statistical analyses included principal component analysis, linkage disequilibrium analysis, and univariate linear mixed models to identify significant single-nucleotide polymorphisms and candidate genes. (3) Results: Forty-five significantly related SNPs and 17 potential candidate genes associated with litter traits were identified. Individuals with the TT genotype at SNP rs341909772 showed an increase of 1.24 in the number of piglets born alive (NBA) and 1.25 in the number of healthy births (NHBs) compared with those with the CC genotype. (4) Conclusions: The SNPs and genes identified in this study offer insights into the genetics of reproductive traits in the Large White pig, potentially guiding the development of breeding strategies to improve litter size.

Integration Linkage Mapping and Comparative Transcriptome Analysis to Dissect the Genetic Basis of Rice Salt Tolerance Associated with the Germination Stage.

Soil salinity poses a serious threat to rice production. The salt tolerance of rice at the germination stage is one of the major determinants of stable stand establishment, which is very important for direct seeding in saline soil. The complexity and polygenic nature of salt tolerance have limited the efficiency of discovering and cloning key genes in rice. In this study, an RIL population with an ultra-high-density genetic map was employed to investigate the salt-tolerant genetic basis in rice, and a total of 20 QTLs were detected, including a major and stable QTL (qRCL3-1). Subsequently, salt-specific DEGs from a comparative transcriptome analysis were overlaid onto annotated genes located on a stable QTL interval, and eight putative candidate genes were further identified. Finally, from the sequence alignment and variant analysis, OsCam1-1 was confirmed to be the most promising candidate gene for regulating salinity tolerance in rice. This study provides important information for elucidating the genetic and molecular basis of rice salt tolerance at the germination stage, and the genes detected here will be useful for improvements in rice salt tolerance.

Deciphering the genetic basis of behavioral traits in dogs: Observed-trait GWAS and latent-trait GWAS analysis reveal key genes and variants.

Dogs exhibit remarkable phenotypic diversity, particularly in behavioral traits, making them an excellent model for studying the genetic basis of complex behaviors. Behavioral traits such as aggression and fear are highly heritable among different dog breeds, but their genetic basis is largely unknown. We used the genome-wide association study (GWAS) to identify candidate genes associated with nine behavioral traits including; stranger-directed aggression (SDA), owner-directed aggression (ODA), dog-directed aggression (DDA), stranger-directed fear (SDF), nonsocial fear (NF), dog-directed fear (DDF), touch sensitivity (TS), separation-related behavior (SRB) and attachment attention-seeking (AAS). The observed behavioral traits were collected from 38,714 to 40,460 individuals across 108 modern dog breeds. We performed a GWAS based on a latent trait extracted using the confirmatory factor analysis (CFA) method with nine observable behavioral traits and compared the results with those from the GWAS of the observed traits. Using both observed-trait and latent-trait GWAS, we identified 41 significant SNPs that were common between both GWAS methods, of which 26 were pleiotropic, as well as 10 SNPs unique to the latent-trait GWAS, and 5 SNPs unique to the observed-trait GWAS discovered. These SNPs were associated with 21 genes in latent-trait GWAS and 22 genes in the observed-trait GWAS, with 19 genes shared by both. According to previous studies, some of the genes from this study have been reported to be related to behavioral and neurological functions in dogs. In the human population, these identified genes play a role in either the formation of the nervous system or are linked to various mental health conditions. Taken together, our findings suggest that latent-trait GWAS for behavioral traits in dogs identifies significant latent genes that are neurologically prioritized.

Identification of candidate genes associating with soybean cyst nematode in soybean (Glycine max L.) using BSA-seq.

Soybean cyst nematode disease represents the major soil-borne disease of soybean. Identifying disease-resistant genes in soybean has a substantial impact on breeding of disease-resistant crops and genetic improvement. The present work created the F2 population with the disease-resistant line H-10 and disease-susceptible line Chidou4. 30 respective F2disease-resistant and disease-susceptible individuals for forming two DNA pools for whole-genome re-sequencing were selected. As a result, a total of 11,522,230 single nucleotide polymorphism (SNPs) markers from these two parental lines and two mixed pools were obtained. Accordng to SNP-index based association analysis, there were altogether 741 genes out of 99% confidence interval, which were mainly enriched into regions of 38,524,128∼39,849,988 bp with a total length of 1.33 Mb contain 111 genes on chromosome 2, 27,821,012∼29,612,574 bp with a total length of 1.79 Mb contain 92 genes on chromosome 3, 308∼348,214 bp with a total of length 0.35 Mb contain 34 genes on chromosome 10, and 53,867,581∼58,017, 852 bp with a total length of 4.15 Mb contain 504 genes on chromosome 18. Bulk segregant analysis in F2 generations (BSA-seq) was correlated with a disease resistance interval containing 15 genes. Then, using bioinformatics analysis and differential expression analysis, five candidate genes were identified: Glyma.02G211400, Glyma.18G252800, Glyma.18G285800, Glyma.18G287400 and Glyma.18G298200. Our results provides a key basis for analyzing the soybean resistance mechanism against soybean cyst nematode and cloning soybean resistance genes.

Genome-wide dissection of genes shaping inflorescence morphology in 242 Chinese south-north sorghum accessions.

The inflorescences morphology (IM) of sorghum (Sorghum bicolor L. Moench) affects its resistance to pests, diseases, and grain yields. However, the specific genetic factors underlying in IM are not yet fully elucidated. Here we conducted a comprehensive genome-wide association analysis (GWAS) to identify the stable and adaptive Quantitative Trait Loci (QTL) for five IM traits (panicle length, the number of cob nodes, the number of primary branches, the largest length of the primary branch, and panicle type) in a sorghum panel, which adapted to different environments from the south to north in China. Totally, 2,015,850 high quality single nucleotide polymorphisms (SNPs) were obtained. Population structure analysis showed that two distinct genetic sub-populations were divided according to their geographic origin. Seventy-one QTLs distributed in 41 genetic regions on 9 chromosomes were identified. These regions harbored 21 high-confident candidate genes that were homologous to rice domestication genes, including 7 related to IM. Two domestication-related genes (Sobic.003G052700 and Sobic.006G247700) were located into two major QTL regions (QTL3.4721839 and QTL6.58709500) which were identified in multi-environments. Allelic variations in the two genes displayed a geographical pattern, indicating that different IM traits were selected by south and north sorghum breeders, such as south sorghums had long and loose panicles in order to adapt the hot and humid climate, while north sorghums had short and compact panicle to increase planting density and grain yield per unit area due to dry climate. This work provides new breeding strategies and resources for developing locally adapted sorghum varieties.

Genome-Wide Association Studies (GWAS) and Transcriptome Analysis Reveal Male Heterogametic Sex-Determining Regions and Candidate Genes in Northern Snakeheads (Channa argus).

The Northern snakehead (Channa argus) is a significant economic aquaculture species in China. Exhibiting sexual dimorphism in the growth rate between females and males, mono-sex breeding holds substantial value for aquaculture. This study employed GWAS and transcriptome analysis were applied to identify sex determination genomic regions and develop sex-specific markers. A total of 270 single-nucleotide polymorphisms (SNPs) and 31 insertion-deletions (InDels) were identified as being sexually dimorphic through GWAS and fixation index (Fst) scanning. Based on GWAS results, two sex-specific InDel markers were developed, effectively distinguishing genetic sex for XX females, XY males, and YY super-males via (polymerase chain reaction) PCR amplification. A major genomic segment of approximately 115 kb on chromosome 3 (Chr 03) was identified as the sex-determination region. A comparative transcriptome analysis of gonads for three sexes identified 158 overlapping differentially expressed genes (DEGs). Additionally, three sex-related candidate genes were identified near the sex determination region, including id2, sox11, and rnf144a. Further studies are required to elucidate the functions of these genes. Overall, two sex-specific InDel markers support a male heterogametic XX/XY sex-determination system in Northern snakeheads and three candidate genes offer new insights into sex determination and the evolution of sex chromosomes in teleost fish.

Morpho-molecular evaluation for developmental competence of oocytes retrieved through transvaginal ovum pick-up from FSH-stimulated Tharparkar donor cows (Bos indicus).

The study was conducted on indigenous Tharparkar cow (Bos indicus) to evaluate FSH stimulation on follicular attributes, oocyte recovery and morpho-molecular developmental competence parameters concerning oocyte quality. A total of 20 OPU sessions were performed, which included 10 sessions in each FSH stimulated at the dose of 130 µg divided into four sub-doses and non-stimulated. Findings on the size of follicles having ≥6 mm showed a significantly higher, however an opposite trend was observed in the case of smaller sized follicle (<6 mm) between stimulated and non-stimulated respectively. The stimulated cows had a significantly higher number as well as the percentage of oocytes of Grade A, having a diameter ≥120 µm and BCB+VE as compared to the non-stimulated cows. The relative mRNA expression profile of GDF9, BMP15, PCNA and BCL-2 genes was higher and BAX was lower in the FSH-stimulated cow. These results indicated that FSH stimulation before OPU in Bos indicus cows has a significant impact on follicle size, oocyte yield, recovery, and their quality with respect to COC's, diameter and BCB+VE oocytes. Further, a significant increase in the relative mRNA expression levels of GDF9, BMP15 and PCNA genes in the FSH-stimulated group suggests that FSH plays a key role in modulating the expression of these important candidate genes and thus influencing oocyte quality. The higher mRNA expression of BCL-2 genes and concomitantly lower expression of BAX gene in FSH Stimulated cows indicates the protective role of these genes and preventing programmed cell death and thus promoting cell survival, quality and embryo development.

Combined BSA-Seq and RNA-Seq Analysis to Identify Candidate Genes Associated with Aluminum Toxicity in Rapeseed (Brassica napus L.).

Exchangeable aluminum (Al) ions released from acidic soils with pH < 5.5 inhibit root elongation of crops, ultimately leading to yield reduced. It is necessary to identify the quantitative trait locus (QTLs) and candidate genes that confer toxicity resistance to understand the mechanism and improve tolerance of rapeseed. In this study, an F2 segregating population was derived from a cross between Al-tolerance inbred line FDH188 (R178) and -sensitive inbred line FDH152 (S169), and the F2:3 were used as materials to map QTLs associated with the relative elongation of taproot (RET) under Al toxicity stress. Based on bulked segregant analysis sequencing (BSA-seq), three QTLs (qAT-A07-1, qAT-A07-2, and qAT-A09-1) were detected as significantly associated with RET, and 656 candidate genes were screened. By combined BSA and RNA-seq analysis, 55 candidate genes showed differentially expressed, including genes encoding ABC transporter G (ABCG), zinc finger protein, NAC, ethylene-responsive transcription factor (ERF), etc. These genes were probably positive factors in coping with Al toxicity stress in rapeseed. This study provides new insight into exploring the QTLs and candidate genes' response to Al toxicity stress by combined BSA-seq and RNA-seq and is helpful to further research on the mechanism of Al resistance in rapeseed.

Genome-Wide Association Study Reveals the Genetic Architecture of Growth and Meat Production Traits in a Chicken F2 Resource Population.

BACKGROUND/OBJECTIVES: For genomic selection to enhance the efficiency of broiler production, finding SNPs and candidate genes that define the manifestation of main selected traits is essential. We conducted a genome-wide association study (GWAS) for growth and meat productivity traits of roosters from a chicken F2 resource population (n = 152). METHODS: The population was obtained by crossing two breeds with contrasting phenotypes for performance indicators, i.e., Russian White (slow-growing) and Cornish White (fast-growing). The birds were genotyped using the Illumina Chicken 60K SNP iSelect BeadChip. After LD filtering of the data, 54,188 SNPs were employed for the GWAS analysis that allowed us to reveal significant specific associations for phenotypic traits of interest and economic importance. RESULTS: At the threshold value of p < 9.2 × 10-7, 83 SNPs associated with body weight at the age of 28, 42, and 63 days were identified, as well as 171 SNPs associated with meat qualities (average daily gain, slaughter yield, and dressed carcass weight and its components). Moreover, 34 SNPs were associated with a group of three or more traits, including 15 SNPs significant for a group of growth traits and 5 SNPs for a group of meat productivity indicators. Relevant to these detected SNPs, nine prioritized candidate genes associated with the studied traits were revealed, including WNT2, DEPTOR, PPA2, UNC80, DDX51, PAPPA, SSC4D, PTPRU, and TLK2. CONCLUSIONS: The found SNPs and candidate genes can serve as genetic markers for growth and meat performance characteristics in chicken breeding in order to achieve genetic improvement in broiler production.

GWAS for Drought Resilience Traits in Red Clover (Trifolium pratense L.).

Red clover (Trifolium pratense L.) is a well-appreciated grassland crop in temperate climates but suffers from increasingly frequent and severe drought periods. Molecular markers for drought resilience (DR) would benefit breeding initiatives for red clover, as would a better understanding of the genes involved in DR. Two previous studies, as follows, have: (1) identified phenotypic DR traits in a diverse set of red clover accessions; and (2) produced genotypic data using a pooled genotyping-by-sequencing (GBS) approach in the same collection. In the present study, we performed genome-wide association studies (GWAS) for DR using the available phenotypic and genotypic data. Single nucleotide polymorphism (SNP) calling was performed using GBS data and the following two red clover genome assemblies: the recent HEN-17 assembly and the Milvus assembly. SNP positions with significant associations were used to delineate flanking regions in both genome assemblies, while functional annotations were retrieved from Medicago truncatula orthologs. GWAS revealed 19 significant SNPs in the HEN-17-derived SNP set, explaining between 5.3 and 23.2% of the phenotypic variation per SNP-trait combination for DR traits. Among the genes in the SNP-flanking regions, we identified candidate genes related to cell wall structuring, genes encoding sugar-modifying proteins, an ureide permease gene, and other genes linked to stress metabolism pathways. GWAS revealed 29 SNPs in the Milvus-derived SNP set that explained substantially more phenotypic variation for DR traits, between 5.3 and 42.3% per SNP-trait combination. Candidate genes included a DEAD-box ATP-dependent RNA helicase gene, a P-loop nucleoside triphosphate hydrolase gene, a Myb/SANT-like DNA-binding domain protein, and an ubiquitin-protein ligase gene. Most accessions in this study are genetically more closely related to the Milvus genotype than to HEN-17, possibly explaining how the Milvus-derived SNP set yielded more robust associations. The Milvus-derived SNP set pinpointed 10 genomic regions that explained more than 25% of the phenotypic variation for DR traits. A possible next step could be the implementation of these SNP markers in practical breeding programs, which would help to improve DR in red clover. Candidate genes could be further characterized in future research to unravel drought stress resilience in red clover in more detail.

Identification of Candidate Genes for Cold Tolerance at Seedling Stage by GWAS in Rice (Oryza sativa L.).

Due to global climate change, cold temperatures have significantly impacted rice production, resulting in reduced yield and quality. In this study, we investigated two traits related to the cold tolerance (CT) of 1992 diverse rice accessions at the seedling stage. Geng accessions exhibited higher levels of CT compared to xian accessions, with the GJ-tmp subgroup displaying the strongest CT. However, extreme CT accessions were also identified within the xian subspecies. Through GWAS analysis based on the survival rate (SR) and leaf score of cold tolerance (SCT), a total of 29 QTLs associated with CT at the seedling stage were identified, among which four QTLs (qSR3.1a, qSR4.1a, qSR11.1x, and qSR12.1a) were found to be important. Furthermore, five candidate genes (LOC_Os03g44760, LOC_Os04g06900, LOC_Os04g07260, LOC_Os11g40610, and LOC_Os12g10710) along with their favorable haplotypes were identified through gene function annotation and haplotype analysis. Pyramiding multiple favorable haplotypes resulted in a significant improvement in CT performance. Subsequently, three selected accessions (CX534, B236, and IRIS_313-8565), carrying different superior alleles for CT, were selected and recommended for molecular breeding for CT using marker-assisted selection (MAS). The findings from this study provide valuable resources for enhancing rice's ability for CT while laying a foundation for the future cloning of novel genes involved in conferring CT.

Comparative transcriptome analysis and meta-QTLs mapping reveal the regulatory mechanism of cold tolerance in rice at the budding stage.

Rice (Oryza sativa L.) is one of the most extensively farmed food crops, but its development and productivity are significantly impacted by cold stress during the budding period. In this study, transcriptome sequencing was conducted on two types of rice: the cold-sensitive indica rice A117 and the substantially cold-tolerant japonica rice B106 under control and cold treatments. Differentially expressed genes between the two materials under cold conditions were analyzed using GO and KEGG enrichment analyses. The results revealed that processes such as the TCA cycle, glycolysis/glycogenesis, oxidative phosphorylation, and glutathione metabolism contribute to B106's cold tolerance. Additionally, an enrichment analysis of cold-induced genes in each material and shared genes identified significant enrichment in pathways such as glutathione metabolism, phenylpropanoid biosynthesis, and photosynthesis-antenna proteins. Initial cold tolerance QTLs at the rice bud stage were collected from published literature, and meta-QTL mapping identified 9 MQTLs. Gene expression profiling led to the identification of 75 potential DEGs within the 9 MQTLs region, from which four candidate genes (Os02g0194100, Os03g0802500, Os05g0129000, and Os07g0462000) were selected using qRT-PCR and gene annotation. These findings provide genetic resources for further research on the molecular mechanisms underlying rice's response to cold stress during the bud stage.

Genetic Foundations of Nellore Traits: A Gene Prioritization and Functional Analyses of Genome-Wide Association Study Results.

The main goal of this study was to pinpoint functional candidate genes associated with multiple economically important traits in Nellore cattle. After quality control, 1830 genomic regions sourced from 52 scientific peer-reviewed publications were used in this study. From these, a total of 8569 positional candidate genes were annotated for reproduction, 11,195 for carcass, 5239 for growth, and 3483 for morphological traits, and used in an over-representation analysis. The significant genes (adjusted p-values < 0.05) identified in the over-representation analysis underwent prioritization analyses, and enrichment analysis of the prioritized over-represented candidate genes was performed. The prioritized candidate genes were GFRA4, RFWD3, SERTAD2, KIZ, REM2, and ANKRD34B for reproduction; RFWD3, TMEM120A, MIEF2, FOXRED2, DUSP29, CARHSP1, OBI1, JOSD1, NOP58, and LOXL1-AS1 for the carcass; ANKRD34B and JOSD1 for growth traits; and no genes were prioritized for morphological traits. The functional analysis pinpointed the following genes: KIZ (plays a crucial role in spindle organization, which is essential in forming a robust mitotic centrosome), DUSP29 (involved in muscle cell differentiation), and JOSD1 (involved in protein deubiquitination, thereby improving growth). The enrichment of the functional candidate genes identified in this study highlights that these genes play an important role in the expression of reproduction, carcass, and growth traits in Nellore cattle.

Quantitative Trait Loci Mapping of Heading Date in Wheat under Phosphorus Stress Conditions.

Wheat (Triticum aestivum L.) is a crucial cereal crop, contributing around 20% of global caloric intake. However, challenges such as diminishing arable land, water shortages, and climate change threaten wheat production, making yield enhancement crucial for global food security. The heading date (HD) is a critical factor influencing wheat's growth cycle, harvest timing, climate adaptability, and yield. Understanding the genetic determinants of HD is essential for developing high-yield and stable wheat varieties. This study used a doubled haploid (DH) population from a cross between Jinmai 47 and Jinmai 84. QTL analysis of HD was performed under three phosphorus (P) treatments (low, medium, and normal) across six environments, using Wheat15K high-density SNP technology. The study identified 39 QTLs for HD, distributed across ten chromosomes, accounting for 2.39% to 29.52% of the phenotypic variance. Notably, five stable and major QTLs (Qhd.saw-3A.7, Qhd.saw-3A.8, Qhd.saw-3A.9, Qhd.saw-4A.4, and Qhd.saw-4D.3) were consistently detected across varying P conditions. The additive effects of these major QTLs showed that favorable alleles significantly delayed HD. There was a clear trend of increasing HD delay as the number of favorable alleles increased. Among them, Qhd.saw-3A.8, Qhd.saw-3A.9, and Qhd.saw-4D.3 were identified as novel QTLs with no prior reports of HD QTLs/genes in their respective intervals. Candidate gene analysis highlighted seven highly expressed genes related to Ca2+ transport, hormone signaling, glycosylation, and zinc finger proteins, likely involved in HD regulation. This research elucidates the genetic basis of wheat HD under P stress, providing critical insights for breeding high-yield, stable wheat varieties suited to low-P environments.