A novel 22-bp InDel within FGF7 gene is significantly associated with growth traits in goat

Fibroblast growth factor 7 (FGF7) is involved in lipid metabolism, which is considered as a candidate gene with close relation with muscle development by eGWAs and RNA-Seq analyses. To date, limited research has been conducted on the relationship between FGF7 gene and growth traits. The main objective of this work was to further investigate the association between novel InDel within FGF7 gene and growth traits in goat. Herein, FGF7 mRNA expression levels were investigated in various Fuqing goat tissues. We found that FGF7 gene was expressed in six adult goat tissues with the highest mRNA levels in adipose tissue. This result suggested that FGF7 gene might play a critical role in fat deposition. We also detected potential polymorphisms in Fuqing, Nubian and Jianyang Daer breeds. A 22-bp InDel polymorphism in FGF7 gene was detected in 396 goats and the three genotypes were designated as II, ID, and DD. Correlation analysis revealed that InDel polymorphism was significantly associated with growth traits (P < 0.05). Goats with genotypes ID and/or II had superior growth traits compared to those with genotype DD. In summary, our findings suggested that the 22-bp InDel within FGF7 gene could act as a molecular marker to improve the growth traits of goats in breeding programs.

Association analysis of the sorting nexin 29 (SNX29) gene copy number variations with growth traits in Diannan small-ear (DSE) pigs

SNX29 is a potential functional gene associated with meat production traits. Previous studies have shown that SNX29 copy number variation (CNV) could be implicated with phenotype in goats. However, in Diannan small-ear (DSE) pigs, the genetic impact of SNX29 CNV on growth traits remains unclear. Therefore, this study investigated the associations between SNX29 CNVs (CNV10810 and CNV10811) and growth traits in 415 DSE pigs. The results revealed that the CNV10810 mutation was significantly associated with backfat thickness in DSE pigs at 12 and 15 months old (P < 0.05), while the CNV10811 mutation had significant effects on various growth traits at 6 and 12 months old, particularly for body weight, body height, back height and backfat thickness (P < 0.05 or P < 0.001). In conclusion, our results confirm that SNX29 CNV plays a role in regulating growth and development in pigs, thus suggesting its potential application for pig breeding programmes.

Association analysis between Acetyl-Coenzyme A Acyltransferase-1 gene polymorphism and growth traits in Xiangsu pigs

Introduction

Acetyl-Coenzyme A Acyltransferase-1 (ACAA1) is a peroxisomal acyltransferase involved in fatty acid metabolism. Current evidence does not precisely reveal the effect of the ACAA1 gene on pig growth performance.

Methods

The present study assessed the mRNA expression levels of the ACAA1 gene in the heart, liver, spleen, lung, kidney of 6-month-old Xiangsu pigs and in the longissimus dorsi muscle at different growth stages (newborn, 6 months and 12 months of age) using RT-qPCR. The relationship between single-nucleotide polymorphisms (SNPs) of ACAA1 gene and growth traits in 6-month-old and 12-month-old Xiangsu pigs was investigated on 184 healthy Xiangsu pigs using Sanger sequencing.

Results

The ACAA1 gene was expressed in heart, liver, spleen, lung, kidney, and longissimus dorsi muscle of 6-month-old pigs, with the highest level of expression in the liver. ACAA1 gene expression in the longissimus dorsi muscle decreased with age (p < 0.01). In addition, four SNPs were identified in the ACAA1 gene, including exon g.48810 A>G (rs343060194), intron g.51546 T>C (rs319197012), exon g.55035 T>C (rs333279910), and exon g.55088 C>T (rs322138947). Hardy-Weinberg equilibrium (p > 0.05) was found for the four SNPs, and linkage disequilibrium (LD) analysis revealed a strong LD between g.55035 T>C (rs333279910) and g.55088 C>T (rs322138947) (r 2 = 1.000). Association analysis showed that g.48810 A>G (rs343060194), g.51546 T>C (rs319197012), g.55035 T>C (rs333279910), and g.55088 C>T (rs322138947) varied in body weight, body length, body height, abdominal circumference, leg and hip circumference and living backfat thickness between 6-month-old and 12-month-old Xiangsu pigs.

Conclusion

These findings strongly demonstrate that the ACAA1 gene can be exploited for marker-assisted selection to improve growth-related phenotypes in Xiangsu pigs and present new candidate genes for molecular pig breeding.

Effects of Salt Stress on Physiological and Agronomic Traits of Rice Genotypes with Contrasting Salt Tolerance

Salinity is one of the major constraints to crop production. Rice is a main staple food and is highly sensitive to salinity. This study aimed to elucidate the effects of salt stress on physiological and agronomic traits of rice genotypes with contrasting salt tolerance. Six contrasting rice genotypes (DJWJ, JFX, NSIC, HKN, XD2H and HHZ), including three salt-tolerant and three salt-sensitive rice genotypes, were grown under two different salt concentrations (0 and 100 mmol L-1 NaCl solution). The results showed that growth, physiological and yield-related traits of both salt-sensitive and salt-tolerant rice were significantly affected by salt stress. In general, plant height, tiller number, dry weight and relative growth rate showed 15.7%, 11.2%, 25.2% and 24.6% more reduction in salt-sensitive rice than in salt-tolerant rice, respectively. On the contrary, antioxidant enzyme activity (superoxide dismutase, peroxidase, catalase), osmotic adjustment substances (proline, soluble protein, malondialdehyde (MDA)) and Na+ content were significantly increased under salt stress, and the increase was far higher in salt-tolerant rice except for MDA. Furthermore, grain yield and yield components significantly decreased under salt stress. Overall, the salt-sensitive rice genotypes showed a 15.3% greater reduction in grain yield, 5.1% reduction in spikelets per panicle, 7.4% reduction in grain-filling percentage and 6.1% reduction in grain weight compared to salt-tolerant genotypes under salt stress. However, a modest gap showed a decline in panicles (22.2% vs. 22.8%) and total spikelets (45.4% vs. 42.1%) between salt-sensitive and salt-tolerant rice under salinity conditions. This study revealed that the yield advantage of salt-tolerant rice was partially caused by more biomass accumulation, growth rate, strong antioxidant capacity and osmotic adjustment ability under salt stress, which contributed to more spikelets per panicle, high grain-filling percentage and grain weight. The results of this study could be helpful in understanding the physiological mechanism of contrasting rice genotypes' responses to salt stress and to the breeding of salt-tolerant rice.

Are two beneficial mutations (p.Q249R and 90-bp Indel) within the ovine BMPRIB gene associated with growth traits?

Background

The problem of achieving economic efficiency in sheep breeding can be largely solved by increasing sheep productivity. Recently, the BMPRIB gene has been revealed by GWAS as a potential candidate gene for sheep body morphometric traits. Therefore, the present study aimed to investigate whether genetic polymorphisms (p.Q249R SNP and 90-bp deletion) in the BMPRIB gene are associated with sheep growth traits.

Methods

PCR-based genotyping was performed on 1,875 sheep, including 1,191 Guiqian semi-fine wool (GQSFW), 560 Luxi Blackhead (LXBH), 55 Lanzhou fat-tailed (LZFT), and 69 Weining (WN) sheep. Genotype-phenotype association was assessed using the independent samples t-test and ANOVA. The significance level was set at αoriginal < 0.05. The threshold p-value for significance was adjusted after correction for multiple comparisons using the Bonferroni correction.

Results

After the Bonferroni correction, it was found that individuals with FecB+/FecB+ genotypes of the p.Q249R had significantly better growth traits in LXBH ewe lambs, including the body length, chest width, paunch girth, cannon circumference, and hip width (P<0.0005). Meanwhile, associations were observed between 90-bp deletion polymorphism and several growth traits (body length, body height, chest depth, and canon circumference) in GQSFW ewe adults after the Bonferroni correction (P < 0.0002), and individuals with the "DD" genotypes had greater growth traits.

Conclusion

Our findings align with the experimental observations from GWAS, which identified the BMPRIB gene as a potential candidate gene for body measurement traits. These findings not only confirm the previous study's results but also expand on them. Therefore, further investigations regarding the impact of BMPRIB polymorphisms on growth traits are necessary in other sheep breeds.

Genomic Prediction of Growth Traits in Yorkshire Pigs of Different Reference Group Sizes Using Different Estimated Breeding Value Models

The need for sufficient reference population data poses a significant challenge in breeding programs aimed at improving pig farming on a small to medium scale. To overcome this hurdle, investigating the advantages of combing reference populations of varying sizes is crucial for enhancing the accuracy of the genomic estimated breeding value (GEBV). Genomic selection (GS) in populations with limited reference data can be optimized by combining populations of the same breed or related breeds. This study focused on understanding the effect of combing different reference group sizes on the accuracy of GS for determining the growth effectiveness and percentage of lean meat in Yorkshire pigs. Specifically, our study investigated two important traits: the age at 100 kg live weight (AGE100) and the backfat thickness at 100 kg live weight (BF100). This research assessed the efficiency of genomic prediction (GP) using different GEBV models across three Yorkshire populations with varying genetic backgrounds. The GeneSeek 50K GGP porcine high-density array was used for genotyping. A total of 2295 Yorkshire pigs were included, representing three Yorkshire pig populations with different genetic backgrounds-295 from Danish (small) lines from Huaibei City, Anhui Province, 500 from Canadian (medium) lines from Lixin County, Anhui Province, and 1500 from American (large) lines from Shanghai. To evaluate the impact of different population combination scenarios on the GS accuracy, three approaches were explored: (1) combining all three populations for prediction, (2) combining two populations to predict the third, and (3) predicting each population independently. Five GEBV models, including three Bayesian models (BayesA, BayesB, and BayesC), the genomic best linear unbiased prediction (GBLUP) model, and single-step GBLUP (ssGBLUP) were implemented through 20 repetitions of five-fold cross-validation (CV). The results indicate that predicting one target population using the other two populations yielded the highest accuracy, providing a novel approach for improving the genomic selection accuracy in Yorkshire pigs. In this study, it was found that using different populations of the same breed to predict small- and medium-sized herds might be effective in improving the GEBV. This investigation highlights the significance of incorporating population combinations in genetic models for predicting the breeding value, particularly for pig farmers confronted with resource limitations.

Genomic prediction based on preselected single-nucleotide polymorphisms from genome-wide association study and imputed whole-genome sequence data annotation for growth traits in Duroc pigs

The use of whole-genome sequence (WGS) data is expected to improve genomic prediction (GP) power of complex traits because it may contain mutations that in strong linkage disequilibrium pattern with causal mutations. However, a few previous studies have shown no or small improvement in prediction accuracy using WGS data. Incorporating prior biological information into GP seems to be an attractive strategy that might improve prediction accuracy. In this study, a total of 6334 pigs were genotyped using 50K chips and subsequently imputed to the WGS level. This cohort includes two prior discovery populations that comprise 294 Landrace pigs and 186 Duroc pigs, as well as two validation populations that consist of 3770 American Duroc pigs and 2084 Canadian Duroc pigs. Then we used annotation information and genome-wide association study (GWAS) from the WGS data to make GP for six growth traits in two Duroc pig populations. Based on variant annotation, we partitioned different genomic classes, such as intron, intergenic, and untranslated regions, for imputed WGS data. Based on GWAS results of WGS data, we obtained trait-associated single-nucleotide polymorphisms (SNPs). We then applied the genomic feature best linear unbiased prediction (GFBLUP) and genomic best linear unbiased prediction (GBLUP) models to estimate the genomic estimated breeding values for growth traits with these different variant panels, including six genomic classes and trait-associated SNPs. Compared with 50K chip data, GBLUP with imputed WGS data had no increase in prediction accuracy. Using only annotations resulted in no increase in prediction accuracy compared to GBLUP with 50K, but adding annotation information into the GFBLUP model with imputed WGS data could improve the prediction accuracy with increases of 0.00%-2.82%. In conclusion, a GFBLUP model that incorporated prior biological information might increase the advantage of using imputed WGS data for GP.

Genome-wide association study of growth traits and validation of key mutations (MSTN c.C861T) associated with the muscle mass of meat pigeons

Selective breeding of meat pigeons is primarily based on growth traits, especially muscle mass (MM). Identification of functional genes and molecular markers of growth and slaughter traits through a genome-wide association study (GWAS) will help to elucidate the underlying molecular mechanisms and provide a theoretical basis for the selective breeding of meat pigeons. The phenotypic data of body weight (BW) and body size (BS) of 556 meat pigeons at 52 and 80 weeks of age were collected. In total, 160 434 high-quality single nucleotide polymorphism sites were obtained by restriction site-associated DNA sequencing. The GWAS analysis revealed that MSTN, IGF2BP3 and NCAPG/LCORL were important candidate genes affecting the growth traits of meat pigeons. IGF2BP3 and NCAPG/LCORL were highly correlated to BW and BS, which are related to overall growth and development, while MSTN was associated with pectoral thickness and BW. Phenotypic association validation with the use of two meat pigeon populations found that the MSTN mutation c.C861T determines the MM. These results provide new insights into the genetic mechanisms underlying phenotypic variations of growth traits and MM in commercial meat pigeons. The identified markers and genes provide a theoretical basis for the selective breeding of meat pigeons.

Multiple Tissues Transcriptome of Zig-Zag Eel (Mastacembelus armatus) with Different Growth Rates

In order to explore the main regulatory genes and related pathways of growth traits, transcriptome sequencing was first performed on the brain, liver, and muscle tissues of 3-month-old M. armatus with different growth rates. By comparative transcriptome analysis of fast-growing and slow-growing groups of M. armatus, a total of 2887 DEGs were screened, of which 59 up-regulated genes and 105 down-regulated genes were detected in the brain, 146 up-regulated genes and 202 down-regulated genes were detected in the liver, and 529 up-regulated genes and 1846 down-regulated genes were detected in muscle, including insulin-like growth factor binding protein 1a (IGFBP1A), insulin-like growth factor binding protein 1b (IGFBP1B), myosin, light chain 1 (MYL1), and myoglobin (MB). Through Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, we identified a total of 288 significantly enriched GO entries and 68 significantly enriched KEGG pathways related to growth, such as skeletal muscle tissue development, insulin-like growth factor binding, and the mitotic cell cycle. These key genes and signaling pathways may play a key role in regulating the growth of M. armatus. Digging into the regulatory mechanisms of these key genes will provide a theoretical basis for further exploration of the molecular mechanisms related to the growth and development of M. armatus, and help to breed new varieties of M. armatus with rapid growth.

Estimation of (Co) Variance Components and Genetic Parameters for Pre- and Post-Weaning Growth Traits in Dağlıç Sheep

The goal of this study was to estimate (co) variance components and genetic parameters for pre- and post-weaning growth traits in Dağlıç sheep, considering the direct additive genetic, maternal genetic, and maternal permanent environmental effects, with different statistical models. The information of 21,735 native Dağlıç lambs born between 2011 and 2021 was used to estimate (co) variance components by the Average Information-Restricted Maximum Likelihood algorithm. The results showed that the most suitable model was Model 3 for birth weight (BW), average daily gain (ADG), and weaning weight (WW). Model 4 was the most appropriate for weight at three (W3), weight at six (W6), and weight at twelve months of age (W12). The direct heritabilities for BW, W3, ADG, WW, W6, and W12 were 0.35 ± 0.02, 0.36 ± 0.03, 0.27 ± 0.02, 0.22 ± 0.02, 0.47 ± 0.05, and 0.47 ± 0.05, respectively. Genetic and phenotypic correlations amongst the traits were in the range of 0.103 ± 0.008 to 0.995 ± 0.002. These results can be used for the improvement of growth traits in the Dağlıç breed of sheep through selection.

The 12-bp indel in the SMAD family member 2 gene is associated with goat growth traits

SMAD family member 2 (SMAD2) is a member of the TGFβ signaling pathway and functions as an essential regulator in the processes of development, cell proliferation, and bone formation. A previous observation reported that a 12-bp deletion of this gene affected the litter size in goats. However, according to our knowledge, no study has reported an association between this polymorphism and goat body measurement traits. The purpose of this study was to investigate the association of the insertion/deletion (indel) within the SMAD2 gene with the growth traits of goats. The indel polymorphism was found to be significantly associated with chest width and bust (p < 0.05), while cannon circumference was significantly the strongest compared to other traits (p < 0.01) and individuals with the DD genotypes were more dominant genotypes than other genotypes. In summary, we found evidence that the 12-bp indel within the SMAD2 gene could improve goat body measurement traits, paving the way for marker-assisted selection in the field of goat genetics and breeding.

Detection of small sequence variations within the goat GHR gene and its effects on growth traits

Growth hormone receptor (GHR) gene is considered to be an important candidate gene in growth traits. Therefore, the purpose of this study was to detect whether there were potential indel variations in the GHR gene that were related to the growth traits of the Shaanbei white cashmere goats (SBWC). In this study, genomic DNA from 931 healthy SBWC individuals were used to verify the relationship between the indel of the GHR gene and growth traits. Two indel variants, P49-bp indel in intron 1 and P1410-bp indel in 3'-UTR, were confirmed. Association analyses demonstrated that these two indel polymorphism loci were associated with the chest circumference and chest width of SBWC. Additionally, for the P49-bp and P1410-bp indel loci, the ID and II genotypes were dominant genotypes, respectively. Moreover, the genotypic distributions of these two indel loci in SBWC were significantly different from those in three other Chinese indigenous goat breeds (HNBG, GZDG and IMWC) (p < 0.05). Taken together, two indel loci (P49-bp indel and P1410-bp indel) both significantly affected the growth traits of goats. This illustrated that these two indel loci might be the potential DNA marker for use in improving the selection and breeding of goats.

Detection of single nucleotide polymorphism in HTR4 and its relationship with growth traits in sheep

In this study, a single nucleotide polymorphism of HTR4 (hydroxytryptamine receptor 4) was detected using DNA sequencing and KASPar (Kompetitive Allele-Specific PCR) technique with the aim of analyzing its effect on growth traits in 1102 sheep. A synonymous mutation g.101220 C > T located on the fifth intron of the ovis HTR4 gene was detected, and association analysis showed that this mutation was significantly associated with growth traits in sheep (p ＜.05), with TT genotypes having significantly lower body weight, height, length and chest circumference than TC and CC genotypes. It showed that the polymorphism of this locus was significantly associated with growth traits in sheep. In addition, qRT-PCR results showed that HTR4 was expressed in different tissues of sheep. It is highly expressed in the liver, spleen and duodenum. As important metabolic, immune and digestive absorption organs in animals, the above tissues can regulate the excitability of intestinal smooth muscle by participating in the body metabolism and nutrient metabolism of sheep, so that sheep can show better growth characteristics. In conclusion, the polymorphic locus identified in HTR4 gene can be used as candidate molecular marker in sheep breeding.

Novel polymorphism at KLF15 gene and its association with growth traits in Hu sheep

Growth traits are important economic characteristics of livestock and poultry. In the present study, the expression features of KLF15 and the relationship between KLF15 gene polymorphisms and growth traits in Hu sheep were investigated by using real-time quantitative PCR technology (qPCR), Sanger sequencing, and Kaspar genotyping technology. The qPCR results showed that the KLF15 gene is expressed widely in the tested tissues of Hu sheep, and the expression level of the KLF15 gene in the heart and the muscle was significantly higher than in other tissues (p < 0.05). Missense mutation c.62565119 A > G was found in KLF15, and an association analysis showed that it was correlated with the growth traits (body weight, body height, and body length) of Hu sheep (p < 0.05). The body weight, body height, and body length of the sheep carrying the AA genotype were remarkably higher than those of the GG and AG genotypes (p < 0.05). These results showed that novel polymorphisms at the KLF15 gene can be used as a genetic marker of growth traits of Hu sheep.

Insertion/deletion (Indel) variant of the goat RORA gene is associated with growth traits

RAR related orphan receptor A (RORA), which encodes the retinoid-acid-related orphan receptor alpha (RORα), is a clock gene found in skeletal muscle. Several studies have shown that RORα plays an important role in bone formation, suggesting that RORA gene may take part in the regulation of growth and development. The purpose of this research is to study the insertion/deletion (indel) variations of the RORA gene and investigate the relationship with the growth traits of Shaanbei white cashmere (SBWC) goats. Herein, the current study identified that the P4-11-bp and P11-28-bp deletion sites are polymorphic among 12 pairs of primers within the RORA gene in the SBWC goats (n = 641). Moreover, the P11-28-bp deletion locus was significantly related to the body height (p = 0.046), height at hip cross (p = 0.012), and body length (p = 0.003). Both of P4-11-bp and P11-28-bp indels showed the moderate genetic diversity (0.25 Collapse

Key Words

• RAR related orphan receptor A (RORA)
• clock gene
• goat
• growth traits
• insertion/deletion

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MESH Headings

• Pregnancy
• Female
• Animals
• Litter Size/genetics
• Goats/physiology
• INDEL Mutation/genetics
• Phenotype

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Affiliation(s)

Qian Zhou College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
Huina Hu College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
Yuta Yang College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
Yuxin Kang College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
Xianyong Lan College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
Xianfeng Wu Institute of Animal Husbandry and Veterinary, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
Zhengang Guo College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China Animal Husbandry and Veterinary Science Institute of Bijie city, Bijie, Guizhou, China
Chuanying Pan College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China

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Copy number variations of LRRFIP1 gene and the relationship with growth traits in four Chinese sheep

CNVs (copy number variations) are the novel and common structural variants that could cover entire genes found in plenty of species. CNV may influence economically important traits or disease susceptibility in livestock species. Based on the whole genome resequencing results, we found that there was a CNV region on the LRRFIP1 gene. Then we used qPCR to detect the copy number type distribution in 553 individuals of four sheep breeds and used them for association analysis. The results showed that: (1) In the CKS, the sheep with gain type had a larger heart girth (p = 0.049). (2) For the HS, the CNV could significantly affect rump breadth (p = 0.037) and circumference of the cannon (p = 0.035). And the sheep with median type showed better performance in rump breadth and circumference of cannon. (3) At the STHS, the CNV was significantly correlated with chest width (p = 0.000) with loss type as the most favorable CNV type. Meanwhile, the best was the loss type, and the lowest was the median. (4) This CNV had no significant effect on the LTHS. So, the CNV of LRRFIP1 was related to the growth traits of these three sheep breeds and it may be used as a molecular marker for sheep.

Copy number variation of bovine S100A7 as a positional candidate affected body measurements

Beef production is closely related to the national economy and the attention has been paid to the improvement of beef cattle by molecular markers associated. Copy number variations (CNVs) recently have been gained many researches and recognized as an important source of genetic variation. Extensive studies have indicated that CNVs have effects on a large range of economic traits by a wide range of gene copy number alteration. S100A7 is a member of S100 family which is a famous family of Ca2+-binding proteins. S100A7 plays a crucial role in many important phenotypes (progress) including inflammatory diseases, psoriasis, obesity, etc. The aim of our study was to explore the phenotypic effects of CNV located in the S100A7 gene of bovine chromosome 3. We detected S100A7 CNV by qPCR in different cattle breeds, including Qinchuan cattle, Yunling cattle, Xianan cattle and a crossbred group Pinan. The copy number was identified as gain, normal and loss type, our results showed that the gain type was the main type in three types of S100A7 CNV of the whole tested breeds. After CNV detection, association analysis between S100A7 CNV and growth traits was carried out in four cattle breeds. We found significant effects of the CNV on cattle growth traits with differently preferred CNV types such as gain type with better chest depth (p = 0.043) in QC, loss type with better body length (p = 0.008) and rump width (p = 0.014) in YL, normal with better chest girth (p = 0.001), gain with better waist width (p = 0.001) and rump width (p = 0.044) in PN. These results suggested that the S100A7 CNV could affect the phenotypic traits and be used as a promising genetic marker for cattle molecular breeding.

Identification of polymorphic loci in OSMR and GHR genes and analysis of their association with growth traits in sheep

The aim of this study was to analyze the effect of OSMR and GHR genes polymorphisms on growth traits in sheep. The single nucleotide polymorphisms of sheep OSMR and GHR genes were identified by DNA sequencing technology. A total of two intronic mutations g.2443 T > C and g.170196 A > G were identified in OSMR and GHR, respectively. Correlation analysis was carried out between the obtained genotypes and the growth traits of sheep. The results showed that at the OSMR g.2443 T > C locus, the body weight, chest circumference and cannon circumference of the TT genotype sheep were significantly higher than those of the CC genotype sheep (p < .05). At the GHR g.170196 A > G locus, the body weight, body length, chest circumference and cannon circumference of the AA genotype sheep were significantly higher than those of the AG genotype and GG genotype sheep (p < .05). Moreover, the body weight of sheep of combination TTOSMR/AAGHR genotype was significantly higher than that of other combination genotypes (p < .05). Therefore, we believe that the polymorphic sites identified in the OSMR and GHR genes can be used as candidate molecular markers for breeding good traits in sheep.

Investigation of the association between goat DNMT3B gene polymorphism and growth traits

The DNA methyltransferase 3 beta (DNMT3B) gene is key for DNA methylation and has been well recognized in regulating growth and development. A previous observation indicated that an 11-bp indel of DNMT3B affected the reproductive traits in goats, yet the effect of this polymorphism on body measurement traits in goats has not been reported. This study aims to investigate the associations between DNMT3B gene polymorphism and goat growth traits. We investigated this 11-bp indel in 2184 goats and three genotypes have been found in Shaanbei white cashmere goat (SBWC): insertion/insertion (II), deletion/deletion (DD) and insertion/deletion (ID). Only ID and DD genotypes were detected in Nubian goats and Guizhou heima goat (GZHM). The allele frequencies analyzed revealed that the 'D' allele frequencies were higher in all three goat breeds. Further association analysis demonstrated that this indel is markedly associated with the cannon circumference (CC) and cannon circumference index (CCI) of SBWC and cannon circumference (CC) of Nubian goats (p < .05). The CC and CCI are essential indicators to measure the growth status of goats. In summary, our study sheds some light on the potential impact of the 11-bp indel polymorphism of the DNMT3B gene on improving the growth traits in goats.

Association analysis of indels in the VISFATIN gene with five cattle breeds and their growth traits

VISFATIN is an adipose cytokine that has been proved to correlate with growth and development traits. In a previous study from our lab, two insertion/deletions (indels; including a 35-bp insertion at its intron 4 and a 6-bp deletion in intron 5) were identified within the VISFATIN gene. To validate these indels and evaluate their association with growth traits in Chinese cattle, a total of 413 samples from four Chinese indigenous breeds and 217 samples from Chinese breeds were detected. Three genotypes (WW, WI and II) at intron 4 were detected based on the 35-bp insertion (allele I) or deletion (allele W) and showed moderate polymorphism in all samples. Two genotypes (WW and WD) at intron 5 were detected based on the 6-bp deletion (allele D) or insertion (allele W) in Xianan (XN) cattle and Jinnan (JN) cattle population but showed poor polymorphisms. Association analysis illustrated that the indel at intron 4 is significantly associated with chest girth, rump length and body weight in Ji'an (JA) cattle and the indel at intron 5 can cause a significant difference in rump length in JN cattle. To our knowledge, it is the first time it has been shown that indels within the VISFATIN gene are associated with growth traits in the two Chinese indigenous cattle breeds. These findings suggest that the VISFATIN gene can be used as a molecular marker for JN and JA cattle breeding.

Polymorphism and expression level of the FADS3 gene and associated with the growth traits in Hu sheep

Growth traits are the economically important traits of sheep, and screening for genes related to growth and development is helpful for the genetic improvement of ovine growth traits. The fatty acid desaturase 3 (FADS3) is one of the important genes affecting the synthesis and accumulation of polyunsaturated fatty acids in animals. In this study, the expression levels of the FADS3 gene and polymorphism of the FADS3 gene associated with growth traits in Hu sheep were detected using quantitative real-time PCR (qRT-PCR), Sanger sequencing, and KAspar assay. The result showed that the expression levels of the FADS3 gene were widely expressed in all tissues, and the expression level of FADS3 in the lung was significantly higher than in other tissues (p < .05). Then, the polymorphism locus g. 2918 A > C was detected in intron 2 of the FADS3 gene, and associated analysis showed that the mutation in the FADS3 gene was associated significantly with growth traits (including body weight, body height, body length, and chest circumference, p < .05). Therefore, individuals with AA genotype showed significantly better growth traits than those with CC genotype, and FADS3 gene could be a candidate gene for improving growth traits in Hu sheep.

Screening of InDel variants in PRDM6, myostatin and IGF2BP1 genes and association analysis with body measurement traits in Malabari and Attappadi black goats

An insertion/deletion (InDel) polymorphism study of PR/SET domain family 6 (PRDM6), myostatin (MSTN) and insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1) genes was conducted in Malabari and Attappady black goats. An association study of identified InDels and body measurement traits was also performed. Body measurements included body length, chest diameter, chest depth, canon circumference, hip width, and hip height at the hip cross. The body trunk index, the body length index, the canon circumference index, and the chest width index were calculated. The Hardy-Weinberg equilibrium (HWE) was tested using a Chi-square test. The observed heterozygosity (Ho), expected heterozygosity (He), and polymorphism information content (PIC) were calculated. A significant difference in body measurements was found across breeds, ages, and breed x age interactions. The PRDM6 InDel was also associated with body measurement traits, such as body height, canon circumference and canon circumference index. In both Malabari and Attappadi black MSTN and PRDM6 InDels were in a state of HWE, while IGF2BP1 InDels were not. Indel markers found in the present study may be used for marker-assisted selection of growth traits among goats.

Association between the copy number variation of CCSER1 gene and growth traits in Chinese Capra hircus (goat) populations

Recently, Coiled-coil serine-rich protein 1 (CCSER1) gene is reported to be related to economic traits in livestock, and become a hotspot. In our study, we detected CCSER1 gene CNV in 693 goats from six breeds (GZB, GZW, AN, BH, HG, TH) by quantitative real-time PCR (qPCR) and the association analysis between the types of CNV and growth traits. Then, CCSER1 gene expression pattern was discovered in seven tissues from NB goats. Our results showed that the CCSER1 gene copy numbers were distributed differently in the aforementioned six breeds. The type of CCSER1 gene CNV was significantly associated with body weight and heart girth traits in GZW goat, in which individuals with deletion type were dominant in body weight trait (P < 0.05), while the normal type individuals were more advantageous in heart girth trait (P < 0.01); and there was a significant association with heart girth in TH goat (P < 0.05), which normal type was the dominant one. The expression profile revealed that CCSER1 gene has the highest level in the lung, followed by the small intestine and heart. In conclusion, our result is dedicated to an in-depth study of the novel CCSER1 gene CNV site and to provide essential information for Chinese goats molecular selective breeding in the future.

Investigation of potential genetic factors for growth traits in yellow-feather broilers using weighted single-step genome-wide association study

Yellow-feather broilers take a large portion of poultry industry in China due to its meat characteristics. Improving the growth traits of yellow-feathered broilers will have great significance for the Chinese poultry market. The current study was designed to investigate the potential genetic factors using the weighted single-step genome-wide association study (wssGWAS) method, which takes consideration of more factors including pedigree, sex, environment and has more accuracy than traditional GWAS. The yellow-feather dwarf chickens from Wens Nanfang Poultry Breeding Co. Ltd. were revolved to recode 9 growth traits: Average daily gain (ADG), body weight (BW) at 45 d, 49 d, 56 d, 63 d, 70 d, 77 d, 84 d, 91 d for analysis. For the results, the region 4.63 to 5.03 Mb on chromosome 15, which was the QTL overlapped in BW45, BW49, BW56, BW63, BW84, might be the crucial genetic region for growth traits. Seven GO terms and 3 KEGG pathways, GO:0005200, GO:0005882, GO:0045111, GO:0099513, GO:0099081, GO:0099512, GO:0099080, KEGG:gga04020, KEGG:gga04540, KEGG:gga04210, were detected to relevant with growth traits. The genes enriched in these biological processes (NRAS, TUBB1, ADORA2B, NTRK3, NGF, TNNC2, F-KER, LOC429492, LOC431325, LOC431324, LOC396480) might have the function in growth of yellow-feather broilers.

Genome-wide association studies and haplotype sharing analysis targeting the growth traits in Yandang partridge chickens

The body size of a chicken is an economically important trait as it directly influences the benefits of the poultry industry, but the relevant genetic mechanisms have not yet been elucidated. In this study, we measured eight growth traits for 94 Yandang partridge chickens, then undertook genome-wide association studies (GWAS) for those traits in using a linear mixed model based on 10× whole genomic sequencing data to better understand the knowledge of the genetic architecture of growth traits. Ninety-four individuals and 7647883 SNPs remained after quality control and removal of the sex chromosomes, and these data were used to carry out a GWAS analysis. The result showed that only one significant single-nucleotide polymorphisms (SNP) locates at 14852873 bp on SSC13 surpassed the genome-wide significance level for Keel length (KL). Through linkage disequilibrium analysis and haplotype sharing analysis, we identified one haplotype underlying the SSC13 significantly associated with KL, which could be selected as a potential candidate haplotype that is used in molecular breeding of Yandang partridge chicken. On the other hand, we have learned from a method called bootstrap testing to verify the reliability of GWAS with small experimental samples, which users can access at https://github.com/xuwenwu24/Bootstrap-test.

Genomic prediction of pig growth traits based on machine learning

This study aimed to assess and compare the performance of different machine learning models in predicting selected pig growth traits and genomic estimated breeding values (GEBV) using automated machine learning, with the goal of optimizing whole-genome evaluation methods in pig breeding. The research employed genomic information, pedigree matrices, fixed effects, and phenotype data from 9968 pigs across multiple companies to derive four optimal machine learning models: deep learning (DL), random forest (RF), gradient boosting machine (GBM), and extreme gradient boosting (XGB). Through 10-fold cross-validation, predictions were made for GEBV and phenotypes of pigs reaching weight milestones (100 kg and 115 kg) with adjustments for backfat and days to weight. The findings indicated that machine learning models exhibited higher accuracy in predicting GEBV compared to phenotypic traits. Notably, GBM demonstrated superior GEBV prediction accuracy, with values of 0.683, 0.710, 0.866, and 0.871 for B100, B115, D100, and D115, respectively, slightly outperforming other methods. In phenotype prediction, GBM emerged as the best-performing model for pigs with B100, B115, D100, and D115 traits, achieving prediction accuracies of 0.547, followed by DL at 0.547, and then XGB with accuracies of 0.672 and 0.670. In terms of model training time, RF required the most time, while GBM and DL fell in between, and XGB demonstrated the shortest training time. In summary, machine learning models obtained through automated techniques exhibited higher GEBV prediction accuracy compared to phenotypic traits. GBM emerged as the overall top performer in terms of prediction accuracy and training time efficiency, while XGB demonstrated the ability to train accurate prediction models within a short timeframe. RF, on the other hand, had longer training times and insufficient accuracy, rendering it unsuitable for predicting pig growth traits and GEBV.

Quantifying physiological trait variation with automated hyperspectral imaging in rice

Advancements in hyperspectral imaging (HSI) together with the establishment of dedicated plant phenotyping facilities worldwide have enabled high-throughput collection of plant spectral images with the aim of inferring target phenotypes. Here, we test the utility of HSI-derived canopy data, which were collected as part of an automated plant phenotyping system, to predict physiological traits in cultivated Asian rice (Oryza sativa). We evaluated 23 genetically diverse rice accessions from two subpopulations under two contrasting nitrogen conditions and measured 14 leaf- and canopy-level parameters to serve as ground-reference observations. HSI-derived data were used to (1) classify treatment groups across multiple vegetative stages using support vector machines (≥ 83% accuracy) and (2) predict leaf-level nitrogen content (N, %, n=88) and carbon to nitrogen ratio (C:N, n=88) with Partial Least Squares Regression (PLSR) following RReliefF wavelength selection (validation: R 2 = 0.797 and RMSEP = 0.264 for N; R 2 = 0.592 and RMSEP = 1.688 for C:N). Results demonstrated that models developed using training data from one rice subpopulation were able to predict N and C:N in the other subpopulation, while models trained on a single treatment group were not able to predict samples from the other treatment. Finally, optimization of PLSR-RReliefF hyperparameters showed that 300-400 wavelengths generally yielded the best model performance with a minimum calibration sample size of 62. Results support the use of canopy-level hyperspectral imaging data to estimate leaf-level N and C:N across diverse rice, and this work highlights the importance of considering calibration set design prior to data collection as well as hyperparameter optimization for model development in future studies.

Detection distribution of CNVs of SNX29 in three goat breeds and their associations with growth traits

As a member of the SNX family, the goat sorting nexin 29 (SNX29) is initially identified as a myogenesis gene. Therefore, this study aimed to examine the polymorphism in the SNX29 gene and its association with growth traits. In this study, we used an online platform to predict the structures of the SNX29 protein and used quantitative real-time PCR to detect potential copy number variation (CNV) in Shaanbei white cashmere (SBWC) goats (n = 541), Guizhou black (GB) goats (n = 48), and Nubian (NB) goats (n = 39). The results showed that goat SNX29 protein belonged to non-secretory protein. Then, five CNVs were detected, and their association with growth traits was analyzed. In SBWC goats, CNV1, CNV3, CNV4, and CNV5 were associated with chest width and body length (P < 0.05). Among them, the CNV1 individuals with gain and loss genotypes were superior to those individuals with a median genotype, but CNV4 and CNV5 of individuals with the median genotype were superior to those with the loss and gain genotypes. In addition, individuals with the gain genotype had superior growth traits in CNV3. In brief, this study suggests that the CNV of SNX29 can be used as a molecular marker in goat breeding.

Co-Expression of JcNAC1- and JcZFP8-Improved Agronomic Traits of Tobacco and Enhanced Drought Resistance through NbbHLH1 and NbbHLH2

Previous studies have identified numerous transcription factors involved in drought response, each of which play different roles in plants. The objective of the present study was to evaluate the effectiveness of two transcription factors on drought response in Jatropha curcas L., JcNAC1 and JcZFP8. The overexpression of these transcription factors in tobacco (Nicotiana benthamiana L.) improved drought resistance, but JcZFP8 delayed germination and JcNAC1 reduced biomass and yield. By constitutively co-expressing these two genes in tobacco, drought resistance was improved, and the negative effects of each of them were overcome. The transgenic plants with double-gene co-expression showed stronger drought tolerance with 1.76-fold greater accumulation of proline and lower H2O2 and malondialdehyde (MDA) content to 43 and 65% of wildtype (WT) levels, respectively. The expression levels of NbbHLH1 and NbbHLH2 genes upregulated linearly with the increased drought tolerance of double genes co-expression plants. In drought conditions, the leaf water contents of bhlh1, bhlh2, and bhlh1bhlh2 deletion mutants obtained by CRISPR-CAS9 knockout technique were maintained at 99%, 97%, and 97% of WT. The bhlh1bhlh2 was found with lower germination rate but with higher reactive oxygen levels (1.64-fold H2O2 and 1.41-fold MDA levels). Thus, the co-expression of two transcription factors with different functions overcame the adverse traits brought by a single gene and enhanced the shared drought-tolerant traits, which can provide guidance on theory and selection of gene combinations for the application of multi-gene co-expression in agriculture in the future.

Assembly of Genome and Resequencing Provide Insights into Genetic Differentiation between Parents of Hulong Hybrid Grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂)

The Hulong hybrid grouper was bred from the brown-marbled grouper (Epinephelus fuscoguttatus) ♀ and the giant grouper (E. lanceolatus) ♂, combining the advantageous traits of both parents. Possessing an excellent performance, this hybrid's cultivation promotes the development of the grouper industry. Its male parent, the giant grouper, possesses the fastest growth and the largest body size among all coral-reef-dwelling fish. This species is not only an economically important species in marine aquaculture, but it is also an ideal male parent in the interspecific crossing of grouper species. In the present study, a high-quality chromosome-level genome of the giant grouper was constructed with a total length of 1.06 Gb, consisting of 24 chromosomes and 69 scaffolds. To analyze the genetic differences between the parents of the Hulong hybrid grouper, the structural variations (SVs) between both parental genomes were detected, and a total of 46,643 SVs were obtained. High-quality SNPs were identified from resequencing data. There were significant differences between the two genomes, and the average FST reached 0.685. A total of 234 highly differentiated regions were detected with an FST > 0.9. The protein-coding genes involved in SVs and highly differentiated regions were significantly enriched in metabolic pathways, including fatty metabolism, carbohydrate metabolism, amino acid metabolism and the TCA cycle. These genes may be related to the differences in feeding preferences and the ability to digest carbohydrates between the two grouper species under natural conditions. In addition, protein-coding genes related to the cell cycle and p53-signaling pathway were also detected. These genes may play important roles in the regulation of body size and growth performance. This research provides genomic resources for further breeding works and evolutionary analyses.

How Can Biological and Chemical Silver Nanoparticles Positively Impact Physio-Chemical and Chloroplast Ultrastructural Characteristics of Vicia faba Seedlings?

Through interactions with plant cells, silver nanoparticles (AgNPs) with both biological and chemical origins can stimulate physiological and metabolic processes in plants. To ensure their safe application in the food chain, it is necessary to investigate their effects on plant systems. Therefore, the effects of chemical AgNPs (chem-AgNPs) and biologically synthesized AgNPs (bio-AgNPs) at different levels (i.e., 0, 10, and 50 ppm) on physiological and biochemical traits {i.e., root and shoot growth traits, photosynthetic pigments (Chl a, Chl b, carotenoids, and total pigments), soluble sugars, total carbohydrates, starch, H₂O₂, and antioxidant enzyme activities} of Vicia faba L. seedlings were investigated. AgNPs were biosynthesized from silver nitrate (AgNO₃) by a green synthesis approach using Jatropha curcas seed extract. The synthesized AgNPs were characterized by UV-vis spectroscopy, transmission electron microscopy (TEM), zeta potential, Fourier-transform infrared spectra (FT-IR), and X-ray diffraction (XRD). The results showed that bio-AgNPs at 10 ppm resulted in the highest growth, physiological, and biological traits of faba bean seedlings in comparison with those obtained from both AgNO₃ and chem-AgNPs treatments. On the other hand, all AgNPs treatments adversely affected the chloroplast ultrastructure, however, fewer negative effects were obtained with the application of 10 ppm bio-AgNPs. In addition, the roots and shoots of seedlings contained the lowest Ag content under different treatments at 10 ppm AgNPs in comparison to the highest level of AgNPs (50 ppm), which indicates that additional studies should be incorporated to ensure safe use of lower concentrations of bio-AgNPs in seed priming. In conclusion, the application of biogenic nanoparticles at 10 ppm can be recommended to enhance plant growth and the productivity of strategic crops.

Goat Pleomorphic Adenoma Gene 1 (PLAG1): mRNA Expression, CNV Detection and Associations with Growth Traits

The pleomorphic adenoma gene 1 (PLAG1) gene, as the major gene responsible for growth, plays a vital role in myogenesis. Meanwhile, the relationship between copy number variation (CNV) of this gene and growth traits in goats remains unclear. Therefore, this study investigated four aspects: bioinformatics analysis, mRNA expression (n = 6), CNV detection (n = 224), and association analysis. The findings indicated that the gene had a large number of conserved motifs, and the gene expression level was higher in fetal goats than in adult goats. Three CNV loci were selected from the database, among which CNV1 was located in the bidirectional promoter region and was associated with goat growth traits. CNV analysis showed that CNV2 and CNV3 of the PLAG1 gene were associated with growth traits such as body weight, heart girth, height at hip cross, and hip width (p < 0.05), with CNV1 loss genotype being the superior genotype, and CNV2 and CNV3 median and gain genotypes of being superior genotypes. This finding further confirms that the PLAG1 gene is the dominant gene for growth traits, which will serve as theoretical guidance for goat breeding.

Estimation of rice seedling growth traits with an end-to-end multi-objective deep learning framework

In recent years, rice seedling raising factories have gradually been promoted in China. The seedlings bred in the factory need to be selected manually and then transplanted to the field. Growth-related traits such as height and biomass are important indicators for quantifying the growth of rice seedlings. Nowadays, the development of image-based plant phenotyping has received increasing attention, however, there is still room for improvement in plant phenotyping methods to meet the demand for rapid, robust and low-cost extraction of phenotypic measurements from images in environmentally-controlled plant factories. In this study, a method based on convolutional neural networks (CNNs) and digital images was applied to estimate the growth of rice seedlings in a controlled environment. Specifically, an end-to-end framework consisting of hybrid CNNs took color images, scaling factor and image acquisition distance as input and directly predicted the shoot height (SH) and shoot fresh weight (SFW) after image segmentation. The results on the rice seedlings dataset collected by different optical sensors demonstrated that the proposed model outperformed compared random forest (RF) and regression CNN models (RCNN). The model achieved R² values of 0.980 and 0.717, and normalized root mean square error (NRMSE) values of 2.64% and 17.23%, respectively. The hybrid CNNs method can learn the relationship between digital images and seedling growth traits, promising to provide a convenient and flexible estimation tool for the non-destructive monitoring of seedling growth in controlled environments.

Research Note: Association of VIPR-1 gene polymorphism with growth traits in meat type Japanese quail (Coturnix Japonica)

This study aimed to analyze the polymorphism of the vasoactive intestinal peptide receptor-1 (VIPR-1) gene and its association with growth traits in quail using the PCR-RFLP and sequencing techniques. Genomic DNA was extracted from blood samples of 36 female Savimalt (SV) quails and 49 female French Giant (FG) quails. Growth traits were measured and used for VIPR-1 gene analysis, as body weight (BW), tibia length (TL), chest width (CW), chest depth (CD), sternum length (SL), body length (BL), and tibia circumference (TC). The results showed that 2 SNPs (BsrD I and HpyCH4 IV) were detected in exon 4 to 5 and exon 6 to 7 of the VIPR-1 gene, respectively. The results of association showed that the BsrD I site was not significantly associated with growth traits at 3 or 5 wk of age in the SV strain (P < 0.05), while the BsrD I site was significantly associated with BL at 3 or 5 wk of age in FG (P < 0.05). The HpyCH4 IV site was significantly associated with TL, CW, CD, SL, and BL at 3 wk of age in the SV strain (P < 0.05), while the HpyCH4 IV site was significantly correlated with BW, CW, SL, and BL at 5 wk of age in SV (P < 0.05). The HpyCH4 IV site was significantly associated with TL and TC at 3 wk of age in FG (P < 0.05), while the HpyCH4 IV site was significantly associated with TC at 5 wk of age in FG (P < 0.05). Four haplotype combinations based on 2 SNPs showed significantly association with BW, CW, CD, SL, BL, and TC at 3 or 5 wk of age in SV (P < 0.05). There was not significant association between 3 haplotype combinations with growth trait at 3 or 5 wk of age in FG (P > 0.05). In conclusion, the VIPR-1 gene could be used as a molecular genetic marker to improve growth traits in quail.

Early Growth and Development and Nonlinear Model Fitting Analysis of Ashidan Yak

Understanding animal growth plays an important role in improving animal genetics and breeding. In order to explore the early growth and development law of Ashidan yak, the body weight (BW), wither height (WH), body oblique length (BL) and chest girth (CG) of 260 female Ashidan yaks were measured. These individuals grew under grazing conditions, and growth traits were measured at 6, 12, 18 and 30 months of age. Then the absolute growth and relative growth of Ashidan yak were calculated, and five nonlinear models (Logistic model, Gompertz model, Brody model, von Bertalanffy model and Richards model) were used to fit the growth curve of Ashidan yak. The fitting effect of the model was evaluated according to MSE, AIC and BIC. The results showed that the growth rate of Ashidan yak was the fastest from 12 to 18 months old, and the growth was slow or even stagnant from 6 to 12 months old. The AIC and BIC values of the Richards model were the lowest among the five models, with an AIC value of 4543.98 and a BIC value of 4563.19. The Richards model estimated body weight at 155.642 kg. In summary, the growth rate of female Ashidan yak changes with the seasons, growing faster in warm seasons and slower in cold seasons. Richards model is the best model to describe the growth curve of female Ashidan yak in five nonlinear models.

Arbuscular Mycorrhizal Fungi and Compost-Based Biostimulants Enhance Fitness, Physiological Responses, Yield, and Quality Traits of Drought-Stressed Tomato Plants

Climate change-driven water resource constraints cause tomatoes to suffer from drought. The use of biostimulants has emerged as an important approach to enhancing resilience to drought. However, the roles of biostimulants in the physicochemical characteristics of tomatoes in response to drought are poorly understood. In this study, we evaluated the ability of arbuscular mycorrhizal fungi (AMF) and compost (versus NPK application) to improve the agro-physiology, yield, and fruit quality of tomato plants and their tolerance to drought by comparing them with conventional chemical fertilizers (NPK). Under drought conditions, plant growth traits associated with yield and fruit bioactive compounds (carotenoids: 73%; lycopene: 53%; polyphenols: 310%; and flavonoids: 158%) were increased in the AMF-tomato treatment. Compost significantly enhanced sugars (ca. 60%) and protein contents (ca. 20%). Moreover, AMF protected the photosynthetic apparatus from drought-induced oxidative stress, improved photosynthetic efficiency, leaf water potential, and osmolytes, and reduced malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) accumulation by increasing peroxidase (POX) (140%) and polyphenol oxidase (PPO) (340%) activities compared to their controls. Our findings revealed that NPK is an important nutrient-based fertilizer for plant growth and development. However, its efficiency as a fertilizer is quite low. In addition, we highlighted different mechanisms mediated by AMF and compost, inducing drought tolerance in tomato plants.

Increasing genomic prediction accuracy for unphenotyped full-sib families by modeling additive and dominance effects with large datasets in white spruce

INTRODUCTION

Genomic selection is becoming a standard technique in plant breeding and is now being introduced into forest tree breeding. Despite promising results to predict the genetic merit of superior material based on their additive breeding values, many studies and operational programs still neglect non-additive effects and their potential for enhancing genetic gains.

METHODS

Using two large comprehensive datasets totaling 4,066 trees from 146 full-sib families of white spruce (Picea glauca (Moench) Voss), we evaluated the effect of the inclusion of dominance on the precision of genetic parameter estimates and on the accuracy of conventional pedigree-based (ABLUP-AD) and genomic-based (GBLUP-AD) models.

RESULTS

While wood quality traits were mostly additively inherited, considerable non-additive effects and lower heritabilities were detected for growth traits. For growth, GBLUP-AD better partitioned the additive and dominance effects into roughly equal variances, while ABLUP-AD strongly overestimated dominance. The predictive abilities of breeding and total genetic value estimates were similar between ABLUP-AD and GBLUP-AD when predicting individuals from the same families as those included in the training dataset. However, GBLUP-AD outperformed ABLUP-AD when predicting for new unphenotyped families that were not represented in the training dataset, with, on average, 22% and 53% higher predictive ability of breeding and genetic values, respectively. Resampling simulations showed that GBLUP-AD required smaller sample sizes than ABLUP-AD to produce precise estimates of genetic variances and accurate predictions of genetic values. Still, regardless of the method used, large training datasets were needed to estimate additive and non-additive genetic variances precisely.

DISCUSSION

This study highlights the different quantitative genetic architectures between growth and wood traits. Furthermore, the usefulness of genomic additive-dominance models for predicting new families should allow practicing mating allocation to maximize the total genetic values for the propagation of elite material.

Estimates of Genetic Parameters for Direct and Maternal Effects on Pre-Weaning Growth Traits in Turkish Saanen Kids

Data on 4487 Turkish Saanen kids from 176 bucks and 1318 dam-goats, obtained from the Turkish Saanen goats in the Izmir region and collected between 2018 and 2019, were analyzed to examine the effect of genetic and non-genetic factors on growth traits. The average birth weight of the kids was determined as 3.33 ± 0.68 kg, the average W60 was 13.06 ± 2.94 kg, the average WW was 18.38 ± 4.14 kg, and the average PreWDG until weaning was 0.17 ± 0.04 g. Model 1, which does not account for the maternal effect, and Model 2, which includes the maternal effect, were used in the estimation of genetic parameters. The heritability estimates of BW, W60, WW, and PreWDG ranged from 0.05 to 0.59 in both models. It is recommended to consider the maternal effect as well as the environmental factors in the selection program for the best early breeder selection of kids growing alongside their mothers until the weaning period.

The Novel Structural Variation in the GHR Gene Is Associated with Growth Traits in Yaks (Bos grunniens)

The growth hormone receptor (GHR) is a member of the cytokine/hematopoietic factor receptor superfamily, which plays an important role in the growth and development, immunity, and metabolism of animals. This study identified a 246 bp deletion variant in the intronic region of the GHR gene, and three genotypes, including type II, type ID, and type DD, were observed. Genotype analysis of structural variation (SV) was performed on 585 individuals from 14 yak breeds, and it was found that 246 bp deletion was present in each breed. The II genotype was dominant in all yak breeds except for SB yak. The association analysis of gene polymorphisms and growth traits in the ASD yak population showed that the 246 bp SV was significantly associated with body length at 6 months (p < 0.05). GHR messenger RNA (mRNA) was expressed in all the tested tissues, with significantly higher levels in the liver, muscle, and fat than in other organs. The results of transcription activity showed that the luciferase activity of the pGL4.10-DD vector was significantly higher than that of the pGL4.10-II vector (p < 0.05). Additionally, the transcription-factor binding prediction results showed that the SV in the runt-related transcription factor 1 (Runx1) transcription-factor binding site may affect the transcriptional activity of the GHR gene, regulating yak growth and development. This study showed that the novel SV of the GHR gene could be used as a candidate molecular marker for the selection of the early growth trait in ASD yak.

Maternal Rumen Bacteriota Shapes the Offspring Rumen Bacteriota, Affecting the Development of Young Ruminants

The maternal rumen microbiota can affect the infantile rumen microbiota and likely offspring growth, and some rumen microbes are heritable and are associated with host traits. However, little is known about the heritable microbes of the maternal rumen microbiota and their role in and effect on the growth of young ruminants. From analyzing the ruminal bacteriota from 128 Hu sheep dams and their 179 offspring lambs, we identified the potential heritable rumen bacteria and developed random forest prediction models to predict birth weight, weaning weight, and preweaning gain of the young ruminants using rumen bacteria as predictors. We showed that the dams tended to shape the bacteriota of the offspring. About 4.0% of the prevalent amplicon sequence variants (ASVs) of rumen bacteria were heritable (h2 > 0.2 and P < 0.05), and together they accounted for 4.8% and 31.5% of the rumen bacteria in relative abundance in the dams and the lambs, respectively. Heritable bacteria classified to Prevotellaceae appeared to play a key role in the rumen niche and contribute to rumen fermentation and the growth performance of lambs. Lamb growth traits could be successfully predicted using some maternal ASVs, and the accuracy of the predictive models was improved when some ASVs from both dams and their offspring were included. IMPORTANCE Using a study design that enabled direct comparison of the rumen microbiota between sheep dams and their lambs, between littermates, and between sheep dams and lambs from other mothers, we identified the heritable subsets of rumen bacteriota in Hu sheep, some of which may play important roles in affecting the growth traits of young lambs. Some maternal rumen bacteria could help predict the growth traits of the young offspring, and they may assist in breeding of and selection for high-performance sheep.

Utilizing Variants Identified with Multiple Genome-Wide Association Study Methods Optimizes Genomic Selection for Growth Traits in Pigs

Improving the prediction accuracies of economically important traits in genomic selection (GS) is a main objective for researchers and breeders in the livestock industry. This study aims at utilizing potentially functional SNPs and QTLs identified with various genome-wide association study (GWAS) models in GS of pig growth traits. We used three well-established GWAS methods, including the mixed linear model, Bayesian model and meta-analysis, as well as 60K SNP-chip and whole genome sequence (WGS) data from 1734 Yorkshire and 1123 Landrace pigs to detect SNPs related to four growth traits: average daily gain, backfat thickness, body weight and birth weight. A total of 1485 significant loci and 24 candidate genes which are involved in skeletal muscle development, fatty deposition, lipid metabolism and insulin resistance were identified. Compared with using all SNP-chip data, GS with the pre-selected functional SNPs in the standard genomic best linear unbiased prediction (GBLUP), and a two-kernel based GBLUP model yielded average gains in accuracy by 4 to 46% (from 0.19 ± 0.07 to 0.56 ± 0.07) and 5 to 27% (from 0.16 ± 0.06 to 0.57 ± 0.05) for the four traits, respectively, suggesting that the prioritization of preselected functional markers in GS models had the potential to improve prediction accuracies for certain traits in livestock breeding.

Blood transcriptome reveals immune and metabolic-related genes involved in growth of pasteurized colostrum-fed calves

The quality of colostrum is a key factor contributing to healthy calf growth, and pasteurization of colostrum can effectively reduce the counts of pathogenic microorganisms present in the colostrum. Physiological changes in calves fed with pasteurized colostrum have been well characterized, but little is known about the underlying molecular mechanisms. In this study, key genes and functional pathways through which pasteurized colostrum affects calf growth were identified through whole blood RNA sequencing. Our results showed that calves in the pasteurized group (n = 16) had higher body height and daily weight gain than those in the unpasteurized group (n = 16) in all months tested. Importantly, significant differences in body height were observed at 3 and 4 months of age (p < 0.05), and in daily weight gain at 2, 3, and 6 months of age (p < 0.05) between the two groups. Based on whole blood transcriptome data from 6-months old calves, 630 differentially expressed genes (DEGs), of which 235 were upregulated and 395 downregulated, were identified in the pasteurized compared to the unpasteurized colostrum groups. Most of the DEGs have functions in the immune response (e.g., CCL3, CXCL3, and IL1A) and metabolism (e.g., PTX3 and EXTL1). Protein-protein interaction analyses of DEGs revealed three key subnetworks and fifteen core genes, including UBA52 and RPS28, that have roles in protein synthesis, oxidative phosphorylation, and inflammatory responses. Twelve co-expression modules were identified through weighted gene co-expression network analysis. Among them, 17 genes in the two modules that significantly associated with pasteurization were mainly involved in the tricarboxylic acid cycle, NF-kappa B signaling, and NOD-like receptor signaling pathways. Finally, DEGs that underwent alternative splicing in calves fed pasteurized colostrum have roles in the immune response (SLCO4A1, AKR1C4, and MED13L), indicative of potential roles in immune regulation. Results from multiple analytical methods used suggest that differences in calf growth between the pasteurized and unpasteurized groups may be due to differential immune activity. Our data provide new insights into the impact of pasteurization on calf immune and metabolic-related pathways through its effects on gene expression.

An On-Station Analysis of Factors Affecting Growth Traits of Pure Red Maasai and Dorper Sheep Breeds under an Extensive Production System

This comparative study aimed to evaluate genetic and environmental factors’ effects on the growth traits of lambs in Dorper and Red Maasai (RedM) sheep breeds. The data analyzed contained the following measurements: birth weight (Bwt), weaning weight (Wwt), yearling weight (Ywt), birth type (single or twins), and details on each lamb’s dam (dam ID and age) and sire. Except for the RedM, whose birth weight decreased with time, both breeds generally showed an increase in other growth weights across the study period, with yearly variations affecting both breeds. Additionally, analysis by a linear mixed model with restricted maximum likelihood (REML) showed that only breed as a factor significantly (p < 0.05) influenced birth weight; breed, sex, and birth type all significantly (p < 0.05) influenced weaning weight, whereas season, sex, and dam age significantly (p < 0.05) influenced yearling weight. The RedM breed outperformed the Dorper breed in post-weaning growth rate, demonstrating early resilience and adaptation to local environmental factors independent of maternal influence. Breed and non-genetic factors play a vital role in the growth of lambs, and the results of this study offer an opportunity for improved farm management under an extensive production system and selection for the conservation of the indigenous Red Maasai breed.

Effects of common full-sib families on accuracy of genomic prediction for tagging weight in striped catfish Pangasianodon hypophthalmus

Common full-sib families (c ² ) make up a substantial proportion of total phenotypic variation in traits of commercial importance in aquaculture species and omission or inclusion of the c ² resulted in possible changes in genetic parameter estimates and re-ranking of estimated breeding values. However, the impacts of common full-sib families on accuracy of genomic prediction for commercial traits of economic importance are not well known in many species, including aquatic animals. This research explored the impacts of common full-sib families on accuracy of genomic prediction for tagging weight in a population of striped catfish comprising 11,918 fish traced back to the base population (four generations), in which 560 individuals had genotype records of 14,154 SNPs. Our single step genomic best linear unbiased prediction (ssGLBUP) showed that the accuracy of genomic prediction for tagging weight was reduced by 96.5%-130.3% when the common full-sib families were included in statistical models. The reduction in the prediction accuracy was to a smaller extent in multivariate analysis than in univariate models. Imputation of missing genotypes somewhat reduced the upward biases in the prediction accuracy for tagging weight. It is therefore suggested that genomic evaluation models for traits recorded during the early phase of growth development should account for the common full-sib families to minimise possible biases in the accuracy of genomic prediction and hence, selection response.

The ovine HIAT1 gene: mRNA expression, InDel mutations, and growth trait associations

Background

The hippocampal abundant transcript 1 (HIAT1) gene, also known as major facilitator superfamily domain-containing 14A (MFSD14A), encodes for a transmembrane transporter protein and has been previously shown to be associated with milk production in buffalo and sheep breeds, as well as growth traits in chicken and goats. However, tissue level distribution of the ovine HIAT1 gene, as well as its effect on body morphometric traits in sheep, has yet to be studied.

Methods

The HIAT1 mRNA expression profile of Lanzhou fat-tailed (LFT) sheep was determined by quantitative real-time PCR (qPCR). A total of 1498 sheep of three indigenous Chinese sheep breeds were PCR-genotyped for polymorphisms of HIAT1 gene. Student's t-test was used to observe the association between the genotype and sheep morphometric traits.

Results

HIAT1 was widely expressed in all examined tissues, and was particularly abundant in the testis of male LFT sheep. Additionally, a 9-bp insertion mutation (rs1089950828) located within the 5'-upstream region of HIAT1 was investigated in Luxi black-headed (LXBH) sheep and Guiqian semi-fine wool (GSFW) sheep. The wildtype allele frequency 'D' was found to be more prevalent than that of the mutant allele 'I'. Furthermore, low genetic diversity was confirmed in all sampled sheep populations. Subsequent association analyses indicated an association between the 9-bp InDel mutation of interest and the morphometric traits of LXBH and GSFW sheep. Furthermore, yearling ewes with a heterozygous genotype (ID) demonstrated smaller body sizes, while yearling rams and adult ewes with the heterozygous genotype were found to have overall better growth performance.

Conclusion

These findings imply that functional InDel polymorphism (rs1089950828) has the potential to be utilized for marker-assisted selection (MAS) of growth traits in domestic Chinese sheep populations.

Novel Polymorphisms in Caprine Myostatin Gene and its Relationship with Growth Traits in Saburai Does (Capra hircus)

<b>Background and Objective:</b> Saburai goat (<i>Capra hircus</i>) is a crossbred goat from Boer buck (75%) and Ettawa doe (25%) for meat production purposes. This study was carried out to detect the mutation points or Single Nucleotide Polymorphisms (SNPs) in the myostatin (<i>MSTN</i>) gene of Saburai with the forward sequencing method. <b>Materials and Methods:</b> A total of twenty-one blood samples of Saburai does (75% Boer, 25% Ettawa) were collected from the Villager Breeder Center (VBC) at Tanggamus Regency of Lampung Province, Indonesia. The DNA analysis consists of DNA isolation, PCR analysis and sequencing analysis. The record data were used for association study with the mathematical model: Y_ij = μ+G_i+Є_ij. <b>Results:</b> Research showed that one common SNP of g.217_218.indel.TTTTA (5'UTR) and three novel SNPs of c.386G>C (exon 1), g.641_642.indel.T (intron 2) and c.4957G>C (exon 3) were detected in the present study. In this study, a novel SNP on exon 1 and intron 2 of Saburai <i>MSTN</i> gene has a moderate PIC value (>0.30). In addition, a novel SNP on exon 1 and exon 3 of the Saburai <i>MSTN</i> gene was detected as a missense mutation of A55P and A43P, respectively. Goats with the heterozygous genotype have higher growth traits compared to goats with the homozygous genotype. <b>Conclusion:</b> The goats with heterozygous genotypes can be further developed to increase the productivity of Saburai goats.

Disentangling the effects of biomass and productivity in plant competition

The relationship between competition and productivity in plant communities is unclear, and this is likely to be due to (1) a confusion in the literature between productivity and biomass, (2) the lack of studies assessing variation in competition in all combinations of biomass and productivity. We assessed the outcome of plant-plant interactions by removing the neighbors around five focal species in 14 herbaceous communities with contrasting biomasses and productivities: meadows with high biomass and productivity, heathlands with high biomass and low productivity, understory communities of deciduous forests with low biomass and high productivity and calcareous grasslands with low biomass and low productivity. Competition intensity was quantified with the relative interaction index (RII) calculated for both survival and growth of the transplanted targets assessed with the increase in leaf number. To examine which traits better explain variation in competition and what drives variation in diversity, we also quantified litter decomposition rate, species composition and diversity and six morphological traits related to plant size and growth rate for eight dominant species of each community. Our main questions were: (1) Is competition mostly related to biomass or productivity? (2) Which traits of the community dominants better explain variation in competition? (3) Is variation in competition and related traits correlated with variation in diversity? Competition for survival significantly increased with increasing community biomass (but not productivity). In addition, competition for survival increased with the size traits and competitive effects of the dominant species of the communities, whereas diversity decreased. Competition for growth also increased with increasing productivity, but only for high-biomass communities. Additionally, the increase in competition for growth with increasing soil fertility, as measured with litter decomposition rate, was only due to an increase in target growth in plots without neighbors and was unrelated to community competitive effects and species diversity. The results of our study illustrate how the confusion between productivity and biomass could have contributed to the long-standing debate on variation in competition along productivity gradients and its consequence for diversity.

Association Analysis of PRKAA2 and MSMB Polymorphisms and Growth Traits of Xiangsu Hybrid Pigs

In this study, Xiangsu hybrid pig growth traits were evaluated via PRKAA2 and MSMB as candidate genes. Sanger sequencing revealed three mutation sites in PRKAA2, namely, g.42101G>T, g.60146A>T, and g.61455G>A, and all these sites were intronic mutations. Moreover, six mutation sites were identified in MSMB: intronic g.4374G>T, exonic g.4564T>C, exonic g.6378G>A, exonic g.6386C>T, intronic g.8643G>A, and intronic g.8857A>G. Association analysis revealed that g.42101G>T, g.60146A>T, g.61455G>A, g.4374G>T, g.4564T>C, g.6378G>A, g.6386C>T, g.8643G>A, and g.8857A>G showed different relationship patterns among body weight, body length, body height, chest circumference, abdominal circumference, tube circumference, and chest depth. Real-time polymerase chain reaction results revealed that the expression of PRKAA2 was highest in the longissimus dorsi muscle, followed by that in the heart, kidney, liver, lung, and spleen. The expression of MSMB was highest in the spleen, followed by that in the liver, kidney, lung, heart, and longissimus dorsi muscle. These results suggest that PRKAA2 and MSMB can be used in marker-assisted selection to improve growth related traits in Xiangsu hybrid pigs, providing new candidate genes for Pig molecular breeding.

Meta-analysis of genetic parameters for growth traits in meat, wool and dual-purpose sheep breeds in the world using a random-effects model

BACKGROUND

There is large variation in genetic parameters in literature for growth traits in sheep. Reliable estimation of genetic parameters is required for developing breeding programmes.

OBJECTIVES

The aim of this study was to aggregate results of different studies by meta-analysis to improve reliability of estimated parameters.

METHODS

In the current study, 221 papers that have been published between 1995 and 2021 were reviewed. Using a random-effects model in the Comprehensive Meta-Analysis software, direct and maternal heritabilities, as well as, genetic and phenotypic correlations between growth traits were estimated in meat (M), wool (W) and dual-purpose (D) sheep breeds. The growth traits in this study were birth weight, 3-month weight, 6-month weight, 9-month weight and yearling weight.

RESULTS

The combined direct heritability was the lowest for birth weight (0.190 ± 0.004, 0.198 ± 0.003 and 0.196 ± 0.004 for M, W and D breeds, respectively) and the highest for yearling weight (0.264 ± 0.010, 0.304 ± 0.005 and 0.285 ± 0.020 for M, W and D breeds, respectively). The maternal heritability was the lowest for yearling weight (0.085 ± 0.003, 0.055 ± 0.002 and 0.052 ± 0.005 for M, W and D breeds, respectively) and the highest for 6-month weight (0.240 ± 0.088, 0.164 ± 0.001 and 0.162 ± 0.006 for M, W and D breeds, respectively). The phenotypic and genetic correlations were lower between the weights measured at more distant intervals. The lowest genetic correlation was observed between birth weight and yearling weight (0.290 ± 0.051 for W breeds).

CONCLUSIONS

The small standard errors could indicate that the aggregation of results from different studies improved the reliability of estimated parameters and reduced range of 95% confidence intervals. Hence, the results could be used with greater level of confidence in sheep breeding programmes.

Polymorphism, Expression, and Structure Analysis of a Key Gene ARNT in Sheep (Ovis aries)

Growth traits are influential factors that significantly affects the development of the sheep industry. A previous TMT proteomic analysis found that a key protein in the HIF signaling pathway, ARNT, may influence embryonic skeletal muscle growth and development in sheep. The purpose of this study was to better understand the association between the polymorphisms of ARNT and growth traits of sheep, and the potential function of ARNT. Real-time qPCR (qRT-PCR) of ARNT was carried out to compare its expression in different developmental stages of the muscle tissues and primary myoblasts in the Hu, Chinese merino, and Gangba sheep. The genetic variance of ARNT was detected using the Illumina Ovine SNP 50 K and 600 K BeadChip in the Hu and Ujimqin sheep populations, respectively. The CDS sequence of the ARNT gene was cloned in the Hu sheep using PCR technology. Finally, bioinformatic analytical methods were applied to characterize the genes and their hypothetical protein products. The qRT-PCR results showed that the ARNT gene was expressed significantly in the Chinese merino embryo after 85 gestation days (D85) (p < 0.05). Additionally, after the sheep were born, the expression of ARNT was significant at the weaning stage of the Hu sheep (p < 0.01). However, there was no difference in the Gangba sheep.In addition, six SNP loci were screened using 50 K and 600 K BeadChip. We found a significant association between rs413597480 A > G and the Hu sheep weight at weaning and backfat thickness in the 5-month-old sheep (p < 0.05), and four SNP loci (rs162298018 G > C, rs159644025 G > A, rs421351865 G > A, and rs401758103 A > G) were also associated with growth traits in the Ujimqin sheep (p < 0.05). Interestingly, we found that a G > C mutation at 1948 bp in the cloned ARNT CDS sequence of the Hu sheep was the same locus mutation as rs162298018 G > C identified using the 600 K BeadChip, which resulted in a nonconservative missense point mutation, leading to a change from proline to alanine and altering the number of DNA, protein-binding sites, and the α-helix of the ARNT protein. There was a strong linkage disequilibrium between rs162298018 G > C and rs159644025 G > A, and the ARNT protein was conserved among the goat, Hu sheep, and Texel sheep. And, we propose that a putative molecular marker for growth and development in sheep may be the G > C mutation at 1948 bp in the CDS region of the ARNT gene. Our study systematically analyzed the expression, structure, and function of the ARNT gene and its encoded proteins in sheep. This provides a basis for future studies of the regulatory mechanisms of the ARNT gene.