Traits Of Economic Importance Research Articles

Construction of high-density genetic linkage map and QTL mapping for growth performance in black carp (Mylopharyngodon piceus)

Growth related traits controlled by quantitative trait loci (QTL) are important economic traits in aquaculture fish species. In order to dissect these QTL, a high-density genetic linkage map is particularly important. In this study, the first high-density genetic linkage map of black carp ( Mylopharyngodon piceus ) was constructed using one F 1 family comprising of 128 progenies, based on genotyping-by-sequencing (GBS). A total of 10,390 single nucleotide polymorphisms (SNPs) were discovered and genotyped. A number of 4108 high-quality SNPs were assigned to 24 linkage groups (LGs) and the total length of the map was 1708.53 cM with a resolution of 0.51 cM. Conserved syntenic relationship between the high-density linkage map and the zebrafish chromosomes was detected. Relying on this high-density linkage map, 17 suggestive QTL: one for body weight, four for body length, six for body height, and six for body wide, were identified on three linkage groups (LG10, LG17, LG20). The phenotypic variance explained (PVE) by these QTL ranged from 10.9 to 15.5%. The high-density genetic linkage map serves as valuable genomic resources not only for understanding the genomic basis of economically important traits in this fish species, but also for comparative genomics and evolutionary studies of black carp. The identified QTL provide important value for ongoing marker assisted selection (MAS) in this fish. • The first genetic linkage map for black carp with an average resolution of 0.51 cM per locus was constructed using 4197 SNPs • 17 QTL related to body weight, body length, body width and body height were identified on three linkage groups • The LG1 in black carp corresponding to Chr10 and Chr22 in zebrafish genome.

Effect of genetic variants in the SMAD1 and SMAD5 genes promoter on growth and beef quality traits in cattle

The SMAD1 and SMAD5 genes belong to mothers against decapentaplegic proteins family, which participate in the BMP pathway to control skeletal myogenesis and growth. In the present study, we analyzed the associations between polymorphisms of SMAD1 and SMAD5 genes promoter and important economical traits in Qinchuan cattle. Four SNPs in the SMAD1 gene promoter and three SNPs in the SMAD5 promoter were identified by sequencing of 448 Qinchuan cattles. Allelic and frequency analyses of these SNPs resulted in eight haplotypes both in the promoters of the two genes promoter and identified potential cis-regulatory transcription factor (TF) components. In addition, correlation analysis showed that cattle SMAD1 promoter activity of individuals with Hap4 (P < 0.01) was stronger than that of individuals with Hap2. while the transcriptional activity of individuals with Hap3 within SMAD5 gene promoter was significantly (P < 0.01) higher followed by H2. Uniformly, diplotypes H4-H6 of SMAD1 gene and H1-H3 of SMAD5 gene performed significant (P < 0.01) associations with body measurement and improved carcass quality traits. All these results have indicated that polymorphisms in SMAD1 and SMAD5 genes promoter could impact the transcriptional regulation and then affect muscle content in beef cattle. Moreover, both the SMAD1 and SMAD5 genes were expressed ubiquitously in 10 tissues and had higher expression in the longissimus thoracis tissue from 6-month-old and 12-month-old cattle than in cattle of other ages. We can conclude that SMAD1 and SMAD5 genes may play an important role in muscle growth and development, and the variants mapped within SMAD1 and SMAD5 genes can be utilized in molecular marker-assisted selection for cattle carcass quality and body measurement traits in breed improvement programs of Qinchuan cattle.

Assessment of Heterozygosity and Genome-Wide Analysis of Heterozygosity Regions in Two Duroc Pig Populations.

Heterozygosity can effectively reflect the diverse models of population structure and demographic history. However, the genomic distribution of heterozygotes and the correlation between regions of heterozygosity (runs of heterozygosity, ROHet) and phenotypes are largely understudied in livestock. The objective of this study was to identify ROHet in the Duroc pig genome, and investigate the relationships between ROHet and eight important economic traits. Here, we genotyped 3,770 American Duroc (S21) and 2,096 Canadian Duroc (S22) pigs using 50 K single nucleotide polymorphism array to analyze heterozygosity. A total of 145,010 and 84,396 ROHets were characterized for S21 and S22 populations, respectively. ROHet segments were mostly enriched in 1–2 Mb length classification (75.48% in S21 and 72.25% in S22). The average genome length covered by ROHet was 66.53 ± 12.20 Mb in S21 and 73.32 ± 13.77 Mb in S22 pigs. Additionally, we detected 20 and 13 ROHet islands in S21 and S22 pigs. Genes in these genomic regions were mainly involved in the biological processes of immunity and reproduction. Finally, the genome-wide ROHet-phenotypes association analysis revealed that 130 ROHets of S21 and 84 ROHets of S22 were significantly associated with eight economic traits. Among the candidate genes in the significant ROHet regions, 16 genes related to growth, metabolism, and meat quality were considered as candidate genes for important economic traits of pigs. This work preliminarily explores the effect of heterozygosity-rich regions in the pig genome on production performance and provides new insights for subsequent research on pig genetic improvement.

Characterization of Alternative Splicing Events in Porcine Skeletal Muscles with Different Intramuscular Fat Contents.

Meat quality is one of the most important economic traits in pig breeding and production. Intramuscular fat (IMF) is a major factor that improves meat quality. To better understand the alternative splicing (AS) events underlying meat quality, long-read isoform sequencing (Iso-seq) was used to identify differential (D)AS events between the longissimus thoracis (LT) and semitendinosus (ST), which differ in IMF content, together with short-read RNA-seq. Through Iso-seq analysis, we identified a total of 56,789 novel transcripts covering protein-coding genes, lncRNA, and fusion transcripts that were not previously annotated in pigs. We also identified 456,965 AS events, among which 3930 were DAS events, corresponding to 2364 unique genes. Through integrative analysis of Iso-seq and RNA-seq, we identified 1174 differentially expressed genes (DEGs), among which 122 were DAS genes, i.e., DE-DAS genes. There are 12 overlapped pathways between the top 20 DEGs and DE-DAS genes, as revealed by KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, indicating that DE-DAS genes play important roles in the differential phenotype of LT and ST. Further analysis showed that upregulated DE-DAS genes are more important than downregulated ones in IMF deposition. Fatty acid degradation and the PPAR (peroxisome proliferator-activated receptor) signaling pathway were found to be the most important pathways regulating the differential fat deposition of the two muscles. The results update the existing porcine genome annotations and provide data for the in-depth exploration of the mechanisms underlying meat quality and IMF deposition.

Gene-Set Enrichment Analysis for Identifying Genes and Biological Activities Associated with Growth Traits in Dromedaries.

Simple SummaryThis project aimed to find biological themes affecting growth in dromedaries. Candidate SNPs associated with growth were mapped to 22 genes, and 25 significant themes were identified related to growth. The main biological functions included calcium ion binding, protein binding, DNA-binding transcription factor activity, protein kinase activity, tropomyosin binding, myosin complex, actin-binding, ATP binding, receptor signaling pathway via JAK-STAT, and cytokine activity. EFCAB5, MTIF2, MYO3A, TBX15, IFNL3, PREX1, and TMOD3 genes are candidates for improving growth in camel breeding programs.Growth is an important heritable economic trait for dromedaries and necessary for planning a successful breeding program. Until now, genome-wide association studies (GWAS) and QTL-mapping have identified significant single nucleotide polymorphisms (SNPs) associated with growth in domestic animals, but in dromedaries, the number of studies is very low. This project aimed to find biological themes affecting growth in dromedaries. In the first step, 99 candidate SNPs were chosen from a previously established set of SNPs associated with body weight, gain, and birth weight in Iranian dromedaries. Next, 0.5 kb upstream and downstream of each candidate SNP were selected from NCBI (assembly accession: GCA_000803125.3). The annotation of fragments with candidate SNPs regarding the reference genome was retrieved using the Blast2GO tool. Candidate SNPs associated with growth were mapped to 22 genes, and 25 significant biological themes were identified to be related to growth in dromedaries. The main biological functions included calcium ion binding, protein binding, DNA-binding transcription factor activity, protein kinase activity, tropomyosin binding, myosin complex, actin-binding, ATP binding, receptor signaling pathway via JAK-STAT, and cytokine activity. EFCAB5, MTIF2, MYO3A, TBX15, IFNL3, PREX1, and TMOD3 genes are candidates for improving growth in camel breeding programs.

Detection of candidate genes affecting milk production traits in sheep using whole-genome sequencing analysis.

BackgroundArtificial and natural selection for important economic traits and genetic adaptation of the populations to specific environments have led to the changes on the sheep genome. Recent advances in genome sequencing methods have made it possible to use comparative genomics tools to identify genes under selection for traits of economic interest in domestic animals.ObjectivesIn this study, we compared the genomes of Assaf and Awassi sheep breeds with those of the Cambridge, Romanov and British du cher sheep breeds to explore positive selection signatures for milk traits using nucleotide diversity (Pi) and FST statistical methods.MethodsGenome sequences from fourteen sheep with a mean sequence depth of 9.32X per sample were analysed, and a total of 23 million single nucleotide polymorphisms (SNPs) were called and applied for this study. Genomic clustering of breeds was identified using ADMIXTURE software. The FST and Pi values for each SNP were computed between population A (Assaf and Awassi) and population B (Cambridge, British du cher, and Romanov).ResultsThe results of the PCA grouped two classes for these five dairy sheep breeds. The selection signatures analysis displayed 735 and 515 genes from FST and nucleotide diversity (Pi) statistical methods, respectively. Among all these, 12 genes were shared between the two approaches. The most conspicuous genes were related to milk traits, including ST3GAL1 (the synthesis of oligosacáridos), CSN1S1 (milk protein), CSN2 (milk protein), OSBPL8 (fatty acid traits), SLC35A3 (milk fat and protein percentage), VPS13B (total milk production, fat yield, and protein yield), DPY19L1 (peak yield), CCDC152 (lactation persistency and somatic cell count), NT5DC1 (lactation persistency), P4HTM (test day protein), CYTH4 (FAT Production) and METRNL (somatic cell), U1 (milk traits), U6 (milk traits) and 5S_RRNA (milk traits).ConclusionsThe findings provide new insight into the genetic basis of sheep milk properties and can play a role in designing sheep breeding programs incorporating genomic information.

Three novel simple sequence repeats (SSRs) identified by MALDI-TOF-MS method were associated with backfat in pig

Backfat trait is an important economic trait and highly heritable, but difficult to evaluate. Thus, it is of great significance to explore optimal backfat thickness of pigs by using marker-assisted selection (MAS) to speed up its breeding process and improve economic efficiency. This study aimed to investigate the relationship between genetic variations (e.g., SSRs) and backfat of Qinghai Bamei pigs using MALDI-TOF Mass Spectrometry (MALDI-TOF-MS). Herein, five alternative SSR loci (namely V1, V2, V3, V4 and V5) were selected for subsequent detection. The results suggested that 3 (141-, 143- and 145-), 3 (128-, 130- and 132-), 2 (160- and 162-), 2 (136- and 139-) and 3 (170-, 184- and 192-) alleles of V1, V2, V3, V4 and V5 were found, respectively. Subsequent analysis showed that there was linkage equilibrium among five SSRs and Hap19 (13.1%) (141-/132-/160-/139-/192-) had the highest haplotype frequency. Among these five SSR loci, V1, V2 and V3 loci were significantly associated to the backfat of Qinghai Bamei sows. These findings enriched the study of SSRs in Qinghai Bamei pigs, and (AC)n (Chr15:85485851-85485995), (AC)n (Chr10:52724583–52724713) and (TG)n (Chr4:90732644–90732802) could be utilized as the candidate locus for MAS in pig industry. HIGHLIGHTS Five novel SSR loci was identified in pigs through MALDI-TOF MS. V1, V2 and V3 loci was were significantly associated to the backfat of pigs.

Combining ability and gene action for agronomic traits and Fusarium wilt resistance in pigeonpea

ABSTRACT Combining ability analysis is fundamental in breeding programs to select desirable parents and progenies. The objectives of this study were to determine the combining ability effects, and gene action controlling agronomic traits and resistance to Fusarium wilt (FW) caused by Fusarium udum Butler in pigeonpea [Cajanus cajan (L.) Millspaugh]. Twenty-five progenies were developed from 10 selected parents using a 5 × 5 North Carolina Design II. The progenies and their parents were assessed for agronomic traits and FW resistance. The genotypes were subjected to artificial FW infection using a root dip inoculation technique to evaluate seedling resistance. ICEAP 87105 and ICEAP 01285 had significantly negative general combining ability (GCA) effects for days to 75% maturity (DTM), whereas MWPLR 22, Sauma and Mwayiwathualimi had positive GCA effects for grain yield (GYD) in a desirable direction. The study selected the best hybrids such as ICEAP 01285 × MWPLR 14 for early maturity, FW resistance and a high GYD, and TZA 5582 × ICEAP 00554, TZA 5582 × MWPLR 14, and Mwayiwathualimi × MWPLR 22 for FW resistance and a high GYD. The narrow-sense heritability values varied from 27% (number of seeds per plant) to 97% (DTM). Parental lines TZA 5582 and MWPLR 14 made strong contributions to desirable gene combinations that improved agronomic traits in the selected crosses. The new hybrids form novel breeding populations useful in improving the traits of economic importance in pigeonpea.

Evaluation of Muscle Chemical Composition, Amino Acids Profile and Antioxidative Capacity of the Shaziling Pig and its Crossbreeds

Background: Meat quality in pigs is an extremely important economic trait. The Shaziling pig is representative of good meat quality but has been scarcely utilized because of the unpleasant growth rate and lean percentage. Methods: The differences of muscle chemical composition, amino acids profile and antioxidative capacity were evaluated among [(Berkshire × Shaziling) × (Berkshire × Shaziling) (BS × (B × S)], (Berkshire × Shaziling) × Shaziling [(B × S) × S], Shaziling × (Berkshire × Shaziling) [S × (B × S)] and Shaziling (S × S) pigs. Result: Four groups had plentiful contents of mineral elements (Ca, Zn, Na, K, Cu, Mg, Mn) and abundant amino acids content and no obvious differences in diameters of myofibers and adipocytes were found among four groups. In addition, (B × S) × S pigs had the highest crude protein content, possessed comprehensive nutrient in amino acids and showed preferable antioxidative capacity, suggesting that the meat of (B × S) × S pigs has optimal shelf life.

Mini Core Germplasm Collections for Developing Climate Resilient Crop Cultivars and Achieving Enhanced Genetic Gains in Plant Breeding Programs

Crop germplasm diversity contributes to developing improved crop cultivars aimed at increasing crop productivity to meet future food security needs of world. The large size of germplasm collections and lack of reliable information on traits of economic importance has resulted in low use (<1%) of germplasm. To facilitate realization of the potential benefits of germplasm collections to broaden the genetic base of cultivars in many crops, the mini core (~1% of the entire collection) concept was postulated and a development process proposed, to produce resources recognized globally as an “International Public Good” (IPG). Mini core collections have been developed in several crops and new diverse sources of genetic variation identified for biotic and abiotic stresses, agronomic and nutritional traits for use in crop improvement programs. Using genetically diverse sources scientists have developed breeding lines with enhanced trait expression and higher genetic gains. Molecular characterization of germplasm has revealed that phenotypic traits were as effective as molecular markers in sampling allelic diversity to form mini core collections.

Evaluation of Common Bean (Phaseolus vulgaris L.) Germplasm for Agro-Morphological and Yield Traits and Resistance to Bean Common Mosaic Virus (BCMV) in Western Himalayan Kashmir

Kashmir Himalayas abounds in bean genetic resources with adaptive capacity and better quality. In the present study 110 common bean germplasm accessions were evaluated between 2019-2021 for yield traits as well as for BCMV resistance. BCMV is the most common and most destructive disease of beans and can cause a yield loss as high as 100%. Substantial variability was recorded in the material as depicted by broad range and high GCV, PCV and heritability and significant mean squares in ANOVA. Five accessions recorded stable resistance to BCMV while as 11 accessions were moderately resistant. Several genotypes were identified as novel sources of traits in respect of plant architecture, pod and seed traits as well as overall yielding ability. Promising genotypes identified for BCMV resistance as well as other traits of economic importance can be used as stable donors for improving common bean yield and BCMV resistance for sustainable bean farming in the region.

Characterisation of buckwheat (Fagopyrum spp.) diversity of the northwestern Himalayas

Content Knowledge about genetic variability parameters is imperative for improving crop plants for traits of economic importance. This paper reports the characterisation of a large germplasm set of an underutilised pseudocereal Buckwheat endemic to northwestern Himalayas in order to elucidate the nature of variability as well as identify trait specific genotypes for use in buckwheat breeding programmes. Aim The major aim was to estimate the genetic variability of yield and related traits in diverse germplasm lines of buckwheat collected from different regions of the north-western Himalayas. Methods The material was evaluated in a randomised complete block design with five replications at two different locations in SKUAST-K, Shuhama and MAR &amp; ES Izmarg, Gurez, during the years 2020 and 2021. For assessing diversity patterns, the clustering of the germplasm from both locations was done by Tocher’s method. Key results The results indicated significant variability in the buckwheat germplasm for all morphological traits across locations. The phenotypic cofficient of variation and genotypic coefficients of variation (PCV, GCV), broad sense heritability and genetic advance values varied between locations. Pooled across locations, the highest PCV values were recorded for number of primary branches. Heritability ranged from low for number of secondary branches to medium for days to 50% flowering. Conclusion The present study provided valuable insights about the variability and trait diversity in buckwheat germplasm under Northwestern Himalayan conditions. Implications The information on variability parameters can be harnessed to develop an effective breeding strategy for improving buckwheat for traits of economic interest.

Identification of genes related to growth traits from transcriptome profiles of duck breast muscle tissue

The growth and development of duck skeletal muscle is an important economic trait that is genetically regulated. The internal mechanism underlying the regulation of skeletal muscle growth and development in ducks remains unclear. The purpose of this study was to identify candidate genes related to the growth of duck skeletal muscle. RNA-sequencing technology was used to compare the transcriptome of duck breast muscles in an F2 population with the high breast muscle rate (HB) and the low breast muscle rate (LB). A total of 14,522 genes were confirmed to be expressed in the breast muscle, and 173 differentially expressed genes (DEGs) were identified between the HB and LB groups. Functional analysis showed that these DEGs were mainly involved in biological processes and pathways of fat metabolism and muscle growth, especially the FABP3 and MYL4 involved in the PPAR signaling pathway and cardiac muscle contraction pathway. These findings deepened our understanding of the molecular mechanisms involved in muscle growth in ducks and provided a theoretical basis for improving duck production and breeding of ducks.

Large-Scale Whole Genome Sequencing Study Reveals Genetic Architecture and Key Variants for Breast Muscle Weight in Native Chickens.

Breast muscle weight (BrW) is one of the most important economic traits in chicken, and directional breeding for that results in both phenotypic and genetic changes. The Jingxing yellow chicken, including an original (without human-driven selection) line and a selected line (based on selection for increased intramuscular fat content), were used to dissect the genetic architecture and key variants associated with BrW. We detected 1069 high-impact single nucleotide polymorphisms (SNPs) with high conserved score and significant frequency difference between two lines. Based on the annotation result, the ECM-receptor interaction and fatty acid biosynthesis were enriched, and muscle-related genes, including MYOD1, were detected. By performing genome-wide association study for the BrW trait, we defined a major haplotype and two conserved SNPs that affected BrW. By integrated genomic and transcriptomic analysis, IGF2BP1 was identified as the crucial gene associated with BrW. In conclusion, these results offer a new insight into chicken directional selection and provide target genetic markers by which to improve chicken BrW.

Multi-omics analysis reveals the genetic basis of rice fragrance mediated by betaine aldehyde dehydrogenase 2

IntroductionFragrance is an important economic and quality trait in rice. The trait is controlled by the recessive gene betaine aldehyde dehydrogenase 2 (BADH2) via the production of 2-acetyl-1-pyrroline (2AP). ObjectivesVariation in BADH2 was evaluated at the population, genetic, transcriptional, and metabolic levels to obtain insights into fragrance regulation in rice. MethodsWhole-genome resequencing of the Korean World Rice Collection of 475 rice accessions, including 421 breeding lines and 54 wild accessions, was performed. Transcriptome analyses of a subset of 279 accessions, proteome analyses of 64 accessions, and volatile profiling of 421 breeding lines were also performed. ResultsWe identified over 3.1 million high-quality single nucleotide polymorphisms (SNPs) in Korean rice collection. Most SNPs were present in intergenic regions (79%), and 190,148 SNPs (6%) were located in the coding sequence, of which 53% were nonsynonymous. In total, 38 haplotypes were identified in the BADH2 coding region, including four novel haplotypes (one in cultivated and three in wild accessions). Tajima's D values suggested that BADH2 was under balancing selection in japonica rice. Furthermore, we identified 316 expression quantitative trait loci (eQTL), including 185 cis-eQTLs and 131 trans-eQTLs, involved in BADH2 regulation. A protein quantitative trait loci (pQTL) analysis revealed the presence of trans-pQTLs; 13 pQTLs were mapped 1 Mbp from the BADH2 region. Based on variable importance in projection (VIP) scores, 15 volatile compounds, including 2AP, discriminated haplotypes and were potential biomarkers for rice fragrance. ConclusionWe generated a catalog of haplotypes based on a resequencing analysis of a large number of rice accessions. eQTLs and pQTLs associated with BADH2 gene expression and protein accumulation are likely involved in the regulation of 2AP variation in fragrant rice. These data improve our understanding of fragrance and provide valuable information for rice breeding.

GPTransformer: A Transformer-Based Deep Learning Method for Predicting Fusarium Related Traits in Barley.

Fusarium head blight (FHB) incited by Fusarium graminearum Schwabe is a devastating disease of barley and other cereal crops worldwide. Fusarium head blight is associated with trichothecene mycotoxins such as deoxynivalenol (DON), which contaminates grains, making them unfit for malting or animal feed industries. While genetically resistant cultivars offer the best economic and environmentally responsible means to mitigate disease, parent lines with adequate resistance are limited in barley. Resistance breeding based upon quantitative genetic gains has been slow to date, due to intensive labor requirements of disease nurseries. The production of a high-throughput genome-wide molecular marker assembly for barley permits use in development of genomic prediction models for traits of economic importance to this crop. A diverse panel consisting of 400 two-row spring barley lines was assembled to focus on Canadian barley breeding programs. The panel was evaluated for FHB and DON content in three environments and over 2 years. Moreover, it was genotyped using an Illumina Infinium High-Throughput Screening (HTS) iSelect custom beadchip array of single nucleotide polymorphic molecular markers (50 K SNP), where over 23 K molecular markers were polymorphic. Genomic prediction has been demonstrated to successfully reduce FHB and DON content in cereals using various statistical models. Herein, we have studied an alternative method based on machine learning and compare it with a statistical approach. The bi-allelic SNPs represented pairs of alleles and were encoded in two ways: as categorical (–1, 0, 1) or using Hardy-Weinberg probability frequencies. This was followed by selecting essential genomic markers for phenotype prediction. Subsequently, a Transformer-based deep learning algorithm was applied to predict FHB and DON. Apart from the Transformer method, a Residual Fully Connected Neural Network (RFCNN) was also applied. Pearson correlation coefficients were calculated to compare true vs. predicted outputs. Models which included all markers generally showed marginal improvement in prediction. Hardy-Weinberg encoding generally improved correlation for FHB (6.9%) and DON (9.6%) for the Transformer network. This study suggests the potential of the Transformer based method as an alternative to the popular BLUP model for genomic prediction of complex traits such as FHB or DON, having performed equally or better than existing machine learning and statistical methods.

Detection of Novel Variations Related to Litter Size in BMP15 Gene of Luzhong Mutton Sheep (Ovis aries).

Simple SummaryBMP15 is a critical gene in sheep reproduction. Most of its variations have been reported in European sheep. In this study, the entire open reading frame (ORF) region of BMP15 was sequenced in 154 Luzhong mutton sheep. Among 13 identified variations, six were novel. Four SNPs (ENSOART00000010201.1:c.352+342C>A, c.352+1232T>C, c.352+1165A>G and c.353-2036T>A) were significantly associated with litter size, and could be used as candidate genetic markers for improving litter size. The results also suggested possible interaction between BMP15 and FecB/GDF9.Litter size is an important economic trait in the mutton sheep industry. BMP15 is one of the key candidate genes for litter size in sheep. In this study, the entire ORF region of BMP15 was sequenced in 154 Luzhong mutton ewes, and the novel variations were determined. The association between polymorphism in BMP15 and litter size was analyzed using a general linear model. Six out of a total of thirteen variations were identified to be novel. Association analysis indicated that four (SNPs ENSOART00000010201.1:c.352+342C>A, c.352+1232T>C, c.352+1165A>G and c.353-2036T>A) were significantly associated with litter size. The joint analysis among three major genes (BMP15, BMPR1B and GDF9) exhibited significant interaction effects in three combinations (FecB and c.352+1232T>C of BMP15; FecB and c.352+1165A>G of BMP15; c.352+342C>A of BMP15 and ENSOART00000014382.1:c.994G>A of GDF9). For the SNPs c.352+1232T>C and c.352+342C>A, the global distribution of allele frequencies showed that the highest variation frequency occurs in Western Europe. In conclusion, the results demonstrated that BMP15 is a major gene for litter size in Luzhong mutton sheep and candidate SNPs associated with litter size were identified.

Changes in Morphology, Metabolism and Composition of Cuticular Wax in Zucchini Fruit During Postharvest Cold Storage.

Cuticle composition is an important economic trait in agriculture, as it is the first protective barrier of the plant against environmental conditions. The main goal of this work was to study the role of the cuticular wax in maintaining the postharvest quality of zucchini fruit, by comparing two commercial varieties with contrasting behavior against low temperatures; the cold-tolerant variety ‘Natura’, and the cold-sensitive ‘Sinatra’, as well as ‘Sinatra’ fruit with induced-chilling tolerance through a preconditioning treatment (15°C for 48 h). The freshly-harvested ‘Natura’ fruit had a well-detectable cuticle with a significant lower permeability and a subset of 15 up-regulated cuticle-related genes. SEM showed that zucchini epicuticular waxes mainly consisted of round-shaped crystals and clusters of them, and areas with more dense crystal deposition were found in fruit of ‘Natura’ and of preconditioned ‘Sinatra’. The cuticular wax load per surface was higher in ‘Natura’ than in ‘Sinatra’ fruit at harvest and after 14 days at 4°C. In addition, total cuticular wax load only increased in ‘Natura’ and preconditioned ‘Sinatra’ fruit with cold storage. With respect to the chemical composition of the waxes, the most abundant components were alkanes, in both ‘Natura’ and ‘Sinatra’, with similar values at harvest. The total alkane content only increased in ‘Natura’ fruit and in the preconditioned ‘Sinatra’ fruit after cold storage, whereas the amount of total acids decreased, with the lowest values observed in the fruit that showed less chilling injury (CI) and weight loss. Two esters were detected, and their content also decreased with the storage in both varieties, with a greater reduction observed in the cold-tolerant variety in response to low temperature. Gene expression analysis showed significant differences between varieties, especially in CpCER1-like and CpCER3-like genes, involved in alkane production, as well as in the transcription factors CpWIN1-like and CpFUL1-like, associated with cuticle development and epidermal wax accumulation in other species. These results suggest an important role of the alkane biosynthetic pathway and cuticle morphology in maintaining the postharvest quality of zucchini fruit during the storage at low temperatures.

Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array.

Simple SummaryEvaluating population genetic background and genomic selection signatures can provide important insights into the uniqueness and the genetic relationship among breeds. In this study, we analyzed the genetic diversity, population structure, and phylogenetic relationships between Huaxi cattle and its ancestors. The results showed that Huaxi cattle has formed its own unique genetic structure features, which could be clearly distinguished from its ancestors and similar populations. Moreover, some genes associated with important economic traits, including growth and development, reproduction, milk quality, and immune response, were identified by scanning potentially selected genomic regions, which may play an essential role in the excellent environmental adaptability and growth performance of Huaxi cattle. Our study will contribute to the genetic evaluation and rational breeding strategy, and give an extensive reference for understanding the genetic basis of economically important traits in Huaxi cattle.Huaxi cattle, a specialized beef cattle breed in China, has the characteristics of fast growth, high slaughter rate, and net meat rate, good reproductive performance, strong stress resistance, and wide adaptability. In this study, we evaluated the genetic diversity, population structure, and genetic relationships of Huaxi cattle and its ancestor populations at the genome-wide level, as well as detecting the selection signatures of Huaxi cattle. Principal component analysis (PCA) and phylogenetic analysis revealed that Huaxi cattle were obviously separated from other cattle populations. The admixture analysis showed that Huaxi cattle has distinct genetic structures among all populations at K = 4. It can be concluded that Huaxi cattle has formed its own unique genetic features. Using integrated haplotype score (iHS) and composite likelihood ratio (CLR) methods, we identified 143 and 199 potentially selected genes in Huaxi cattle, respectively, among which nine selected genes (KCNK1, PDLIM5, CPXM2, CAPN14, MIR2285D, MYOF, PKDCC, FOXN3, and EHD3) related to ion binding, muscle growth and differentiation, and immunity were detected by both methods. Our study sheds light on the unique genetic feature and phylogenetic relationship of Huaxi cattle, provides a basis for the genetic mechanism analysis of important economic traits, and guides further intensive breeding improvement of Huaxi cattle.

Decorin regulates myostatin and enhances proliferation and differentiation of embryonic myoblasts in Leizhou black duck

Skeletal muscle is one of the most important economic traits in the poultry industry whose development goes through several processes influenced by several candidate genes. This study explored the regulatory role of DCN on MSTN and the influence of these genes on the proliferation and differentiation of embryonic myoblasts in Leizhou black ducks. Embryonic myoblasts were transfected with over-expressing DCN, Si-DCN, and empty vector and cultured for 24h, 48h, and 72h of proliferation and the comparative expression of DCN and MSTN were measured. The results showed that cells transfected with the over-expression DCN had a significantly (P<0.05) higher expression of DCN mRNA than the normal group and the expression of MSTN mRNA showed a downward trend during the proliferation of myoblasts. DCN mRNA expression was lower in cells transfected with Si-DCN than the normal group in all stages of proliferation. While the expression of MSTN in the Si-DCN transfected group was higher than the normal group with a significant (P<0.05) difference at the 72h stage. DCN mRNA increased at the early stage of differentiation but decreased (P>0.05) from the 6th day to the 8th day of differentiation. The level of MSTN increased gradually during the differentiation process of myoblasts until it decreased significantly on the 8th day. These results show that DCN enhances the proliferation and differentiation of Leizhou black duck myoblasts and suppresses MSTN activity.