Genome-wide association study and development of molecular markers for yield and quality traits in peanut (Arachis hypogaea L.).

BACKGROUND: This study aims to decipher the genetic basis governing yield components and quality attributes of peanuts, a critical aspect for advancing molecular breeding techniques. Integrating genotype re-sequencing and phenotypic evaluations of seven yield components and two grain quality traits across four distinct environments allowed for the execution of a genome-wide association study (GWAS). RESULTS: The nine phenotypic traits were all continuous and followed a normal distribution. The broad heritability ranged from 88.09 to 98.08%, and the genotype-environment interaction effects were all significant. There was a highly significant negative correlation between protein content (PC) and oil content (OC). The 10× genome re-sequencing of 199 peanut accessions yielded a total of 631,988 high-quality single nucleotide polymorphisms (SNPs), with 374 significant SNP loci identified in association with the nine traits of interest. Notably, 66 of these pertinent SNPs were detected in multiple environments, and 48 of them were linked to multiple traits of interest. Five loci situated on chromosome 16 (Chr16) exhibited pleiotropic effects on yield traits, accounting for 17.64-32.61% of the observed phenotypic variation. Two loci on Chr08 were found to be strongly associated with protein and oil contents, accounting for 12.86% and 14.06% of their respective phenotypic variations, respectively. Linkage disequilibrium (LD) block analysis of these seven loci unraveled five nonsynonymous variants, leading to the identification of one yield-related candidate gene and two quality-related candidate genes. The correlation between phenotypic variation and SNP loci in these candidate genes was validated by Kompetitive allele-specific PCR (KASP) marker analysis. CONCLUSIONS: Overall, molecular markers were developed for genetic loci associated with yield and quality traits through a GWAS investigation of 199 peanut accessions across four distinct environments. These molecular tools can aid in the development of desirable peanut germplasm with an equilibrium of yield and quality through marker-assisted breeding.

Fashion meets science: how advanced breeding approaches could revolutionize the textile industry.

Natural fibers have garnered considerable attention owing to their desirable textile properties and advantageous effects on human health. Nevertheless, natural fibers lag behind synthetic fibers in terms of both quality and yield, as these attributes are largely genetically determined. In this article, a comprehensive overview of the natural and synthetic fiber production landscape over the last 10 years is presented, with a particular focus on the role of scientific breeding techniques in improving fiber quality traits in key crops like cotton, hemp, ramie, and flax. Additionally, the article delves into cutting-edge genomics-assisted breeding techniques, including QTL mapping, genome-wide association studies, transgenesis, and genome editing, and their potential role in enhancing fiber quality traits in these crops. A user-friendly compendium of 11226 available QTLs and significant marker-trait associations derived from 136 studies, associated with diverse fiber quality traits in these crops is furnished. Furthermore, the potential applications of transcriptomics in these pivotal crops, elucidating the distinct genes implicated in augmenting fiber quality attributes are investigated. Additionally, information on 11257 candidate/characterized or cloned genes sourced from various studies, emphasizing their key role in the development of high-quality fiber crops is collated. Additionally, the review sheds light on the current progress of marker-assisted selection for fiber quality traits in each crop, providing detailed insights into improved cultivars released for different fiber crops. In conclusion, it is asserted that the application of modern breeding tools holds tremendous potential in catalyzing a transformative shift in the textile industry.

Natural fibers possess desirable properties, but they often lag behind synthetic fibers in terms of both quality and quantity. Genomic-assisted breeding has the potential to improve fiber quality traits in cotton, hemp, ramie, and flax. Utilizing available QTLs, marker-trait associations, and candidate genes can contribute to the development of superior fiber crops, underscoring the significance of advanced breeding tools.

Construction of Genetic Map and QTL Mapping for Seed Size and Quality Traits in Soybean (Glycine max L.).

Soybean (Glycine max L.) is the main source of vegetable protein and edible oil for humans, with an average content of about 40% crude protein and 20% crude fat. Soybean yield and quality traits are mostly quantitative traits controlled by multiple genes. The quantitative trait loci (QTL) mapping for yield and quality traits, as well as for the identification of mining-related candidate genes, is of great significance for the molecular breeding and understanding the genetic mechanism. In this study, 186 individual plants of the F2 generation derived from crosses between Changjiangchun 2 and Yushuxian 2 were selected as the mapping population to construct a molecular genetic linkage map. A genetic map containing 445 SSR markers with an average distance of 5.3 cM and a total length of 2375.6 cM was obtained. Based on constructed genetic map, 11 traits including hundred-seed weight (HSW), seed length (SL), seed width (SW), seed length-to-width ratio (SLW), oil content (OIL), protein content (PRO), oleic acid (OA), linoleic acid (LA), linolenic acid (LNA), palmitic acid (PA), stearic acid (SA) of yield and quality were detected by the multiple- d size traits and 113 QTLs related to quality were detected by the multiple QTL model (MQM) mapping method across generations F2, F2:3, F2:4, and F2:5. A total of 71 QTLs related to seed size traits and 113 QTLs related to quality traits were obtained in four generations. With those QTLs, 19 clusters for seed size traits and 20 QTL clusters for quality traits were summarized. Two promising clusters, one related to seed size traits and the other to quality traits, have been identified. The cluster associated with seed size traits spans from position 27876712 to 29009783 on Chromosome 16, while the cluster linked to quality traits spans from position 12575403 to 13875138 on Chromosome 6. Within these intervals, a reference genome of William82 was used for gene searching. A total of 36 candidate genes that may be involved in the regulation of soybean seed size and quality were screened by gene functional annotation and GO enrichment analysis. The results will lay the theoretical and technical foundation for molecularly assisted breeding in soybean.

Genome-Wide Detection of Copy Number Variations and Their Potential Association with Carcass and Meat Quality Traits in Pingliang Red Cattle.

Copy number variation (CNV) serves as a significant source of genetic diversity in mammals and exerts substantial effects on various complex traits. Pingliang red cattle, an outstanding indigenous resource in China, possess remarkable breeding value attributed to their tender meat and superior marbling quality. However, the genetic mechanisms influencing carcass and meat quality traits in Pingliang red cattle are not well understood. We generated a comprehensive genome-wide CNV map for Pingliang red cattle using the GGP Bovine 100K SNP chip. A total of 755 copy number variable regions (CNVRs) spanning 81.03 Mb were identified, accounting for approximately 3.24% of the bovine autosomal genome. Among these, we discovered 270 potentially breed-specific CNVRs in Pingliang red cattle, including 143 gains, 73 losses, and 54 mixed events. Functional annotation analysis revealed significant associations between these specific CNVRs and important traits such as carcass and meat quality, reproduction, exterior traits, growth traits, and health traits. Additionally, our network and transcriptome analysis highlighted CACNA2D1, CYLD, UBXN2B, TG, NADK, and ITGA9 as promising candidate genes associated with carcass weight and intramuscular fat deposition. The current study presents a genome-wide CNV map in Pingliang red cattle, highlighting breed-specific CNVRs, and transcriptome findings provide valuable insights into the underlying genetic characteristics of Pingliang red cattle. These results offer potential avenues for enhancing meat quality through a targeted breeding program.

Exploring genetic diversity and ascertaining genetic loci associated with important fruit quality traits in apple (Malus × domestica Borkh.).

Genetic diversity is the primary source of variability in any crop improvement program, and the diverse germplasm of any crop species represents an important genetic resource for gene or allele mining to meet future needs. Huge genetic and phenotypic diversity is present in the apple gene pool, even though, breeding programs have been mainly focused on a few traits of interests, which have resulted in the reduction of the diversity in the cultivated lines of apple. Therefore, the present study was carried out on 70 diverse apple genotypes with the objective of analyzing the genetic diversity and to identify the genetic loci associated with important fruit quality traits. A total of 140 SSR primers were used to characterize the 70 genotypes of apples, out of which only 88 SSRs were found to be polymorphic. The PIC values varied from 0.03 to 0.75. The value of MI, EMR, and RP varied from 0.03 to 3.5, 0.5 to 5.0, and 1.89 to 6.74, respectively. The dendrogram and structure analysis divided all the genotypes into two main groups. In addition to this, large phenotypic variability was observed for the fruit quality traits under study indicated the suitability of the genotypes for association studies. Altogether 71 novel MTAs were identified for 10 fruit quality traits, of which 15 for fruit length, 15 for fruit diameter, 12 for fruit weight, 2 for total sugar, 2 for TSS, 4 for reducing sugar, 5 for non-reducing sugar, 5 for fruit firmness, 5 for fruit acidity and 6 for anthocyanin, respectively. Consistent with the physicochemical evaluation of traits, there was a significant correlation coefficient among different fruit quality characters, and many common markers were found to be associated with these traits (fruit diameter, length, TSS, total sugar, acidity and anthocyanin, respectively) by using the different modeling techniques (GLM, MLM). The inferred genetic structure, diversity pattern and the identified MTAs will be serving as resourceful grounds for better predictions and understanding of apple genome towards efficient conservation and utilization of apple germplasm for facilitating genetic improvement of fruit quality traits. Furthermore, these findings also suggested that association mapping could be a viable alternative to the conventional QTL mapping approach in apple. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01382-w.

Unlocking the nutritional potential of chickpea: strategies for biofortification and enhanced multinutrient quality.

Chickpea (Cicer arietinum L.) is a vital grain legume, offering an excellent balance of protein, carbohydrates, fats, fiber, essential micronutrients, and vitamins that can contribute to addressing the global population's increasing food and nutritional demands. Chickpea protein offers a balanced source of amino acids with high bioavailability. Moreover, due to its balanced nutrients and affordable price, chickpea is an excellent alternative to animal protein, offering a formidable tool for combating hidden hunger and malnutrition, particularly prevalent in low-income countries. This review examines chickpea's nutritional profile, encompassing protein, amino acids, carbohydrates, fatty acids, micronutrients, vitamins, antioxidant properties, and bioactive compounds of significance in health and pharmaceutical domains. Emphasis is placed on incorporating chickpeas into diets for their myriad health benefits and nutritional richness, aimed at enhancing human protein and micronutrient nutrition. We discuss advances in plant breeding and genomics that have facilitated the discovery of diverse genotypes and key genomic variants/regions/quantitative trait loci contributing to enhanced macro- and micronutrient contents and other quality parameters. Furthermore, we explore the potential of innovative breeding tools such as CRISPR/Cas9 in enhancing chickpea's nutritional profile. Envisioning chickpea as a nutritionally smart crop, we endeavor to safeguard food security, combat hunger and malnutrition, and promote dietary diversity within sustainable agrifood systems.

Preliminary genetic parameter estimates of meat quality traits in Hu sheep.

Because substantial numbers of Chinese consumers are prepared to pay for tender and quality lamb, meat quality traits are becoming more relevant for breeding programs for Chinese sheep breeds. The current study estimated heritabilities and genetic correlations for 13 meat quality traits recorded on lamb loins from Hu sheep. Heritability estimates ranged from 0.04 ± 0.06 for meat redness at 45 min to 0.57 ± 0.10 for drip loss, with most of the meat quality traits having moderate heritabilities. Positive genetic correlations were observed among meat color traits. Intramuscular fat (IMF) was genetically correlated with most meat quality traits, indicating that increasing IMF can favor meat pH, color, and tenderness, but would lead to increased cooking loss. Direct selection to increase IMF of loins is recommended to be included in breeding programs for Hu sheep, as it was more efficient than indirect selection on the other meat quality traits. The genetic parameters presented in this preliminary study provide valuable genetic information needed to design a breeding program aimed at improving the quality of lamb meat from Hu sheep.

The results of meat quality traits and sensory characteristics according to the concentration of androstenone in uncastrated pigs.

Pork quality is determined by several attributes, among which odor and taste are the utmost significant. Therefore, this study was aimed to assess the effects of boar odor hormone concentration on the quality traits and sensory acceptability of pork. A total twenty-six (26) non-castrated 3-way crossbred (Landrace × Yorkshire × Duroc) pigs were selected with an average body weight (ABW) 115.6 kg before to slaughter. The three treatment groups (low, medium and high) were divided according to the androstenone concentration. In experiment 1, for meat quality traits carcass was selected based on androstenone concentration: low (LC, 0.64-0.69 µg/g, n = 9), medium (MC, 0.70-0.99 µg/g, n = 7) and high (HC, 1.00-1.69 µg/g, n = 10). In experiment 2, for sensory evaluation carcasses were also selected based on the abovementioned conditions. Results revealed that androstenone concentration not effect on proximate components, meat quality traits and fatty acids except palmitoleic acid. Sensory evaluation data showed that boar taint and meat boar taint were significantly increased in a concentration-dependent manner from low to high, whereas, gravy and meat flavor preference were significantly increased in LC group than HC group. In addition, correlation analysis showed that boar taint and meat boar taint were positively, and gravy and meat flavor preference were negatively correlated with boar taint hormones. In essence, our findings indicate that androstenone concentration had no effect on meat qualities, but a high concentration of androstenone had a negative effect on the sensory characteristics in uncastrated pigs.

Effects of gender and slaughter age on physicochemical and quality traits of Korean Hanwoo striploin.

Hanwoo beef is in high demand because of its unique flavor, freshness, and high-fat content. However, the longer rearing period required to enhance marbling in Hanwoo cattle has adverse environmental consequences, such as greenhouse gas emissions and overall rearing costs. To address consumer preferences for leaner and healthier meat, the Korean meat industry has recently introduced Hanwoo heifer meat as an alternative source, but its quality traits are still unclear. Nevertheless, there is a limited body of research exploring the impact of Hanwoo gender (steer, heifer, and cow) and their corresponding slaughter ages on meat quality traits. This study looked into how gender affected the physicochemical and qualitative features of Hanwoo striploin at their respective slaughter ages. Results revealed that cow striploin has higher levels of moisture (66.81%) and protein (20.76%), whereas it contains lower levels of fat (10.66%) and cholesterol (34.66 mg/100 g). Regarding the physicochemical properties, cow striploin exhibited significantly lower shear force, color indexes, and soluble collagen (p < 0.05). However, chondroitin (1.19%) and muscle fiber area (1,545.23 µm2) were significantly higher in steer striploin than in heifer and cow (p < 0.05). Cow striploin exhibited significantly higher levels of oleic acid, unsaturated fatty acids (UFAs), and monounsaturated fatty acids (MUFAs) while having lower levels of eicosadienoic acid and atherogenic index compared to the other two groups. Cows and heifers had higher concentrations of amino acid metabolites than striploin from steers. Furthermore, bioactive metabolites such as carnitine and carnosine content were found higher in cow and heifer respectively. Overall, Hanwoo cattle gender influences the qualitative attributes of striploin; nevertheless, compared to steer and heifer striploin, cow striploin is a relatively good source of protein, fatty acid content, and metabolites conducive to a healthy diet.

Haplotype-resolved T2T genome assemblies and pangenome graph of pear reveal diverse patterns of allele-specific expression and the genomic basis of fruit quality traits.

Hybrid crops often exhibit increased yield and greater resilience, yet the genomic mechanism(s) underlying hybrid vigor or heterosis remain unclear, hindering our ability to predict the expression of phenotypic traits in hybrid breeding. Here, we generated haplotype-resolved T2T genome assemblies of two pear hybrid varieties, 'Yuluxiang' (YLX) and 'Hongxiangsu' (HXS), which share the same maternal parent but differ in their paternal parents. We then used these assemblies to explore the genome-scale landscape of allele-specific expression (ASE) and create a pangenome graph for pear. ASE was observed for close to 6000 genes in both hybrid cultivars. A subset of ASE genes related to aspects of fruit quality such as sugars, organic acids, and cuticular wax were identified, suggesting their important contributions to heterosis. Specifically, Ma1, a gene regulating fruit acidity, is absent in the paternal haplotypes of HXS and YLX. A pangenome graph was built based on our assemblies and seven published pear genomes. Resequencing data for 139 cultivated pear genotypes (including 97 genotypes sequenced here) were subsequently aligned to the pangenome graph, revealing numerous structural variant hotspots and selective sweeps during pear diversification. As predicted, the Ma1 allele was found to be absent in varieties with low organic acid content, and this association was functionally validated by Ma1 overexpression in pear fruit and calli. Overall, these results reveal the contributions of ASE to fruit-quality heterosis and provide a robust pangenome reference for high-resolution allele discovery and association mapping.

Metabolomics Uncovers the Mechanisms of Nitrogen Response to Anthocyanins Synthesis and Grain Quality of Colored Grain Wheat (Triticum aestivum L.).

Nitrogen (N) is a key factor for plant growth and affects anthocyanin synthesis. This study aimed to clarify the potential mechanisms of N levels (LN, 0 kg·ha-1; MN, 150 kg·ha-1; HN, 225 kg·ha-1) in anthocyanin synthesis and grain quality of colored grain wheat. HN increased the yield component traits and grain morphology traits in colored grain wheat while decreasing the processing and nutrient quality traits. Most quality traits were significantly negatively correlated with the yield composition and morphological traits. Anthocyanin was more accumulated under LN conditions, but other related yield and morphological traits of colored grain wheat declined. The anthocyanin content was the highest in blue wheat, followed by that in purple wheat. Cyanidin-3-O-(6-O-malonyl-ß-d-glucoside) and cyanidin-3-O-rutinoside were the predominant anthocyanins in blue and purple wheat. The identified anthocyanin-related metabolites were associated with flavonoid biosynthesis, anthocyanin biosynthesis, and secondary metabolite biosynthesis. Therefore, the study provided information for optimizing nitrogen fertilizer management in producing high quality colored wheat and verified the close relationship between anthocyanin and low N condition.

Linkage mapping and genomic prediction of grain quality traits in tropical maize (Zea mays L.).

The suboptimal productivity of maize systems in sub-Saharan Africa (SSA) is a pressing issue, with far-reaching implications for food security, nutrition, and livelihood sustainability within the affected smallholder farming communities. Dissecting the genetic basis of grain protein, starch and oil content can increase our understanding of the governing genetic systems, improve the efficacy of future breeding schemes and optimize the end-use quality of tropical maize. Here, four bi-parental maize populations were evaluated in field trials in Kenya and genotyped with mid-density single nucleotide polymorphism (SNP) markers. Genotypic (G), environmental (E) and G×E variations were found to be significant for all grain quality traits. Broad sense heritabilities exhibited substantial variation (0.18-0.68). Linkage mapping identified multiple quantitative trait loci (QTLs) for the studied grain quality traits: 13, 7, 33, 8 and 2 QTLs for oil content, protein content, starch content, grain texture and kernel weight, respectively. The co-localization of QTLs identified in our research suggests the presence of shared genetic factors or pleiotropic effects, implying that specific genomic regions influence the expression of multiple grain quality traits simultaneously. Genomic prediction accuracies were moderate to high for the studied traits. Our findings highlight the polygenic nature of grain quality traits and demonstrate the potential of genomic selection to enhance genetic gains in maize breeding. Furthermore, the identified genomic regions and single nucleotide polymorphism markers can serve as the groundwork for investigating candidate genes that regulate grain quality traits in tropical maize. This, in turn, can facilitate the implementation of marker-assisted selection (MAS) in breeding programs focused on improving grain nutrient levels.

Meta-QTL analysis and candidate genes for quality traits, mineral content, and abiotic-related traits in wild emmer.

Wild emmer (Triticum turgidum ssp. dicoccoides) genotypes were studied for their high-nutritional value and good tolerance to various types of stress; for this reason, several QTL (quantitative trait loci) studies have been conducted to find favorable alleles to be introgressed into modern wheat cultivars. Given the complexity of the QTL nature, their interaction with the environment, and other QTLs, a small number of genotypes have been used in wheat breeding programs. Meta-QTL (MQTL) analysis helps to simplify the existing QTL information, identifying stable genomic regions and possible candidate genes for further allele introgression. The study aimed to identify stable QTL regions across different environmental conditions and genetic backgrounds using the QTL information of the past 14 years for different traits in wild emmer based upon 17 independent studies. A total of 41 traits were classified as quality traits (16), mineral composition traits (11), abiotic-related traits (13), and disease-related traits (1). The analysis revealed 852 QTLs distributed across all 14 chromosomes of wild emmer, with an average of 61 QTLs per chromosome. Quality traits had the highest number of QTLs (35%), followed by mineral content (33%), abiotic-related traits (28%), and disease-related traits (4%). Grain protein content (GPC) and thousand kernel weight (TKW) were associated with most of the QTLs detected. A total of 43 MQTLs were identified, simplifying the information, and reducing the average confidence interval (CI) from 22.6 to 4.78 cM. These MQTLs were associated with multiple traits across different categories. Nine candidate genes were identified for several stable MQTLs, potentially contributing to traits such as quality, mineral content, and abiotic stress resistance. These genes play essential roles in various plant processes, such as carbohydrate metabolism, nitrogen assimilation, cell wall biogenesis, and cell wall extensibility. Overall, this study underscores the importance of considering MQTL analysis in wheat breeding programs, as it identifies stable genomic regions associated with multiple traits, offering potential solutions for improving wheat varieties under diverse environmental conditions.

Dissecting Genotype by Environment Interactions in Moroccan Wheat: An Advanced Biplot and Heatmap Analysis Unveiling Agronomic, Quality Traits, and Genotypic Stability for Tailored Breeding Strategies.

This five-year study (2016-2021) across diverse Moroccan agro-climatic zones investigated genotype by environment (G × E) interactions in wheat, focusing on variations in agronomic traits and quality attributes such as protein and gluten content. Significant environmental effects were observed on key traits, like yield, thousand kernel weight (TKW), and spikes per square meter (Spk/m2), highlighting environmental factors' role in wheat yield variability. In the Tassaout (TST) location, notable genotypic effects emerged for traits like biomass, underscoring genetic factors' importance in specific contexts, while in Sidi El Aidi (SEA) and Marchouch (MCH), genotypic effects on yield and its components were predominantly absent, indicating a more substantial environmental influence. These findings illustrate the complexity of G × E interactions and the need for breeding strategies considering genetic potential and environmental adaptability, especially given the trade-offs between yield enhancement and quality maintenance. Insights from the biplot and heatmap analyses enhanced the understanding of genotypes' dynamic interactions with environmental factors, establishing a basis for strategic genotype selection and management to optimize wheat yield and quality. This research contributes to sustainable wheat breeding in Morocco, aligning with global efforts to adapt wheat breeding strategies to changing climatic conditions.

Genetic analysis of purple pigmentation in rice seed and vegetative parts - implications on developing high-yielding purple rice (Oryza sativa L.).

Pigmentation in rice grains is an important quality parameter. Purple-coloured rice (Oryza sativa L.) indicates the presence of high anthocyanin with benefits of antioxidant properties. However, the genetic mechanism of grain colour is not fully understood. Therefore, the study focused on understanding pigmentation in grain pericarp and vegetative parts, and its relationship with blast resistance and enhanced grain yield. Three local cultivars from the northeastern region (NER) of India - Chakhao Poireiton (purple), Mang Meikri (light brown), and Kala Joha (white) - along with high-yielding varieties (HYVs) Shasharang (light brown) and Sahbhagi dhan (white) were used to develop biparental populations. The findings suggested that pigmentation in vegetative tissue was governed by the inter-allelic interaction of several genes. Haplotype analysis revealed that Kala3 complemented Kala4 in enhancing purple pigmentation and that Kala4 is not the only gene responsible for purple colour as evident by the presence of a desired allele for markers RID3 and RID4 (Kala4 locus) in Chakhao Poireiton and Kala Joha irrespective of their pericarp colour, implying the involvement of some other additional, unidentified genes/loci. RID3 and RID4 together with RM15191 (Kala3 locus) could be employed as a reliable marker set for marker-assisted selection (MAS). Pericarp colour was strongly correlated with colour in different vegetative parts, but showed a negative correlation with grain yield. Pb1, reported to be associated with panicle blast resistance, contributed to leaf blast resistance. Transgressive segregants for improved pigmentation and high yield were identified. The selection of lines exhibiting coloured pericarp, high anthocyanin content, aroma, blast resistance, and increased yield compared to their respective HYV parents will be valuable resources in the rice breeding programme.

Identify Candidate Genes Associated with the Weight and Egg Quality Traits in Wenshui Green Shell-Laying Chickens by the Copy Number Variation-Based Genome-Wide Association Study.

Copy number variation (CNV), as an essential source of genetic variation, can have an impact on gene expression, genetic diversity, disease susceptibility, and species evolution in animals. To better understand the weight and egg quality traits of chickens, this paper aimed to detect CNVs in Wenshui green shell-laying chickens and conduct a copy number variation regions (CNVRs)-based genome-wide association study (GWAS) to identify variants and candidate genes associated with their weight and egg quality traits to support related breeding efforts. In our paper, we identified 11,035 CNVRs in Wenshui green shell-laying chickens, which collectively spanned a length of 13.1 Mb, representing approximately 1.4% of its autosomal genome. Out of these CNVRs, there were 10,446 loss types, 491 gain types, and 98 mixed types. Notably, two CNVRs showed significant correlations with egg quality, while four CNVRs exhibited significant associations with body weight. These significant CNVRs are located on chromosome 4. Further analysis identified potential candidate genes that influence weight and egg quality traits, including FAM184B, MED28, LAP3, ATOH8, ST3GAL5, LDB2, and SORCS2. In this paper, the CNV map of the Wenshui green shell-laying chicken genome was constructed for the first time through population genotyping. Additionally, CNVRs can be employed as molecular markers to genetically improve chickens' weight and egg quality traits.

Polymorphisms of the SCD1 Gene and Its Association Analysis with Carcass, Meat Quality, Adipogenic Traits, Fatty Acid Composition, and Milk Production Traits in Cattle.

Stearoyl-CoA desaturase-1 (SCD1) is a key enzyme in the biosynthesis of monounsaturated fatty acids and is considered a candidate gene for improving milk and meat quality traits. Sanger sequencing was employed to investigate the genetic polymorphism of the fifth exon and intron of bovine SCD1, revealing four SNPs, g.21272246 A>G, g.21272306 T>C, g.21272422 C>T, and g.21272529 A>G. Further variance analysis and multiple comparisons were conducted to examine the relationship between variation sites and economic traits in Chinese Simmental cattle, as well as milk production traits in Holstein cows. The findings revealed these four loci exhibited significant associations with carcass traits (carcass weight, carcass length, backfat thickness, and waist meat thickness), meat quality (pH value, rib eye area, and marbling score), adipogenic traits (fat score and carcass fat coverage rate), and fatty acid composition (linoleic acid and α-linolenic acid). Furthermore, these loci were additionally found to be significantly associated with average milk yield and milk fat content in cows. In addition, a haplotype analysis of combinations of SNPs showed that H2H3 has a significant association with adipogenic traits and H2H2 was associated with higher levels of linoleic acid and α-linolenic acid than the other combinations. These results suggest that the four SNPs are expected to be prospective genetic markers for the above economic traits. In addition, the function of SNPs in exon 5 of SCD1 on gene expression and protein structure needs to be explored in the future.

Effect of dietary Eucommia ulmoides oliver polysaccharide on immune function and meat quality of Songliao Black Pigs.

Eucommia ulmoides is a traditional Chinese herbal medicine, with pharmacological effects such as lowering blood pressure and enhancing immune function. The effects of dietary Eucommia ulmoides polysaccharide (EUP) on immune function and meat quality were studied in Songliao Black Pigs. Blood lymphocyte counts and percentage, concentrations of serum total protein and of albumin increased, whereas those of urea nitrogen and triglyceride decreased. White blood cell and lymphocyte counts, and serum IgA, IgE, IgG2 a and IFN-γ increased. Average daily weight gain, slaughter weight, lean meat rate and cooked meat rate increased, whereas pH24, feed-weight ratio, fat rate, yellowness (b#) and centrifugal dehydration rate decreased. Transcriptome sequencing of longissimus dorsi muscle detected 32 differentially expressed genes (DEGs), of which 26 were up-regulated and 6 down-regulated. A total of 19 genes were differentially expressed in the four groups, 18 of which were up-regulated. The DEGs included ADAMTS4, PER1, STAC, SERPINE1, FASN, THRSP, SP7 and KRT80 and the protein interaction network showed 20 up-regulated nodes, three down-regulated nodes and 14 DEGs. GO functional annotation and enrichment analysis showed that 34 items were significantly enriched, including transferase activity, actin binding, acetyl coenzyme A, acyl coenzyme A metabolism, adipose tissue development and acyl glycerol homeostasis. KEGG pathway analysis showed that the AMPK and PPAR signaling pathways were enriched. Dietary Eucommia polysaccharide enhanced immune function in Songliao Black Pigs, improved growth and carcass performance, increased the expression of genes related to meat quality traits and improved meat quality.

A Study on the Modifying Effect of Raspberry Seed Oil on Rabbit Meat Quality and Chemical Composition.

The purpose of the study was to determine the effects of raspberry seed oil on the slaughter performance traits, plasma lipid concentration and meat quality of purebred Termond White rabbits (n = 42; 18♂, 24♀). In each group (3 × n = 14; 6♂, 8♀), the experimental animals were fed a complete pelleted feed with constant access to drinking water. Rabbits in the first experimental group received a feed ration enriched with a 1% addition of raspberry seed oil, while rabbits in the second experimental group were given a 2% addition of the same oil. These animals were slaughtered on day 84. The addition of raspberry seed oil did not significantly affect the slaughter performance traits of the rabbits (p > 0.05). It also did not significantly affect the fat content, shear force, hardness, springiness, cohesiveness or chewiness of the meat obtained from the rabbits' longissimus lumborum muscle. However, the experiment showed that the addition of raspberry seed oil had a significant effect on the fatty acid profile of rabbit meat (p ≤ 0.05). Even a small share of this oil in the feed ration significantly increased the level of linoleic acid (p ≤ 0.05). This study showed that feeding pellets containing an oil supplement with a high content of unsaturated fatty acids had a positive effect on rabbits' plasma lipid levels.

Molecular insights into the anti-spoilage effect of salicylic acid in Favorita potato processing.

Salicylic acid is a commonly used anti-spoilage agent to prevent browning and quality degradation during potato processing, yet its precise mechanism remains unclear. This study elucidates the role of StuPPO2, a functional protein in Favorita potato shreds, in relation to the anti-browning and starch degradation effects of 52 SA analogues. By employing molecular docking and Gaussian computing, SA localizes within the hydrophobic cavity of StuPPO2, facilitated by hydroxyl and carboxyl groups. The inhibitory effect depends on the distribution pattern of the maximal electrostatic surface potential, requiring hydroxyl ion potentials of >56 kcal/mol and carboxyl ion potentials of >42 kcal/mol, respectively. Multiomics analysis, corroborated by validation tests, indicates that SA synthetically suppresses activities linked to defense response, root regeneration, starch degradation, glycoalkaloids metabolism, and potato shred discoloration, thereby preserving quality. Furthermore, SA enhances antimicrobial and insect-repellent aromas, thereby countering biotic threats in potato shreds. These collective mechanisms underscore SA's anti-spoilage properties, offering theoretical foundations and potential new anti-browning agents for agricultural preservatives.