Traits Of Economic Importance Research Articles

Yield stability and economic heterosis analysis in newly bred sunflower hybrids throughout diverse agro-ecological zones

Exploration of heterosis is a strategy for enhancing sunflower yield and productivity. In India, the greatest constraints on sunflower production are stagnant and inconsistent yields. By raising them in a variety of ecological conditions, stable per-se performance with the highest yielding potential sunflower hybrids were selected. Sustainable agriculture requires the use of desirable hybrids with high seed yields and oil content too. By making three distinct crossing sets from 32 sunflower genotypes, 11 cytoplasmic male sterility (CMS), and 21 restorer lines, a total of 124 hybrids were developed (comprising both lines and tester). After extensive field evaluation of all hybrids, only eight superior F1s belonging to all three sets, as well as the three national control hybrids KBSH-53, LSFH-171, and DRSH-1, were selected for stability analysis in four agro-ecological regions of West Bengal, India viz., Nimpith, Baruipur, Bankura, and Berhapore. The genetic stability of several phenotypic characters was assessed using statistical models that examine genotype-environment interaction (G × E) in multi-locational yield trials. In this experiment, the performance of hybrids under various environmental circumstances over two-year periods was measured using regression coefficient (bi) and deviations from regression (S2di). With the exception of genotypes CMS-852A × EC-601751 for volume weight (0.9335) and CMS-302A × EC-623011 for head diameter (0.0905) and volume weight (0.6425), all sunflower genotypes for all concerned traits had extremely minor and negligible deviations from regression (S2di), which showed significant values. The genotypes having insignificant values of S2di were more stable. The economic heterosis of these novel hybrids was also quantified. CMS-302A × EC-623011 in which seed yield was recorded 20.90, 20.91, 20.95 and 20.90% higher than DRSH-1 at Nimpith, Baruipur, Bankura and PORS (Berhampur), respectively. The research revealed that CMS-302A × EC-623011, CMS-853A × EC-623027 and P-2–7-1A × EC-512682 exhibited good seed production and stability for critical agronomic parameters in addition to oil content. As a result, the current researches enlighten to find out how stable the expression of important economic traits in sunflower hybrids is.

Genetic Resistance of Switchgrass to Rust Evaluated in a Composite Upland × Lowland Population in Lab and Field Settings

Maintaining low levels of rust incidence (caused by Puccinia novopanici) in switchgrass (Panicum virgatum L.) breeding populations is a priority for the USDA-ARS program engaged in improving cultivars for high biomass yield and quality. Essential to this goal is the unbiased and accurate estimation of genetic parameters to predict the merits of parents and progeny. Spores of the fungus were inoculated in greenhouse-grown seedling progeny of 31 half-sib families in generation 2 (Gen 2) of a composite Summer × Kanlow population for evaluation of rust incidence on the leaves with a 0–9 rating scale. Two parents were later chosen to cross and develop a linkage mapping population as Gen 3. The Gen 2, 3, and Kanlow seedlings were transplanted into the field located near Mead, NE, in early June 2020 and laid out as a replicated row–column design with six blocks of single-row plots of five plants each. The field trial was rated in September 2021 and 2022 with a 0–4 scale. Lab and field data were subjected to univariate linear mixed models via the restricted maximum likelihood to extract the variance components needed to predict the breeding values. The additive genetic variation was substantial (p < 0.01), enough to result in high heritability estimates ranging from 0.42 ± 14 to 0.73 ± 0.09 at the individual and family mean levels. This result implies that rust resistance is under strong genetic control to use mass selection for obtaining satisfactory gains. A possible rust incidence x year interaction was detected with a Spearman correlation of breeding values of −0.38, caused by significant rank changes of the Gen 3 genotypes in 2022 (a high heat and drought year). Genetic gains were predicted to reduce rust incidence scores by at least two points on the rating scale when selecting backwards, and by one point when selecting individual candidates as parents of the next generation. Faster gains (31 and 59%) were realized relative to the second generation by respectively selecting the top 10% of the families in Gen 3 or the top 10% of genotypes within this group. Based on these results, strategies for controlling the incidence of rust will be developed to optimize gains in the other traits of economic importance.

Breeding Practices and Traits of Economic Importance for Indigenous Chicken in South Sudan

The current study aimed at generating essential information on breeding practices and traits of the economic importance of indigenous chicken (IC) farmers in the three historical regions of South Sudan (Bhar el Gazel, Upper Nile and Equatoria). Data on perceived important traits according to farmers (n=385), marketers (n=100) and consumers (n=100) were collected and analyzed through computation of indices which represented the average weight of all ranks of a specific trait. The results of the indices indicated that farmers selected body weight (3.16), disease tolerance (3.02), drought tolerance (2.70) and fast growth rate (2.44) for breeding cocks. For hens, high indices were observed on disease tolerance (2.95), hatchability (2.78), egg size (2.63), and egg number (2.48). Large Baladi (LB) and Naked Neck (Na) genotypes were the dominant genotypes raised by 64.8% and 27.7% of all farmers, respectively, for their superiority in mothering ability (40%), heat tolerance (20%) and disease tolerance (17%). Traits perceived by farmers as the primary economic importance were body weight (0.207), survival rate (0.11), egg yield (0.084) and meat quality (0.084). While marketers perceived body weight (0.234), egg yolk colour (0.150), disease tolerance (0.145), and plumage colour (0.133) as the most important traits, consumers emphasize egg yolk colour (0.202), plumage colour (0.204), and survival rate (0.156) as crucial. Body weight had a positive and favourable significant correlation with growth rate (0.561), egg fertility (0.412), disease tolerance (0.062), and a negative and unfavourable correlation with meat quality (-0.191). Meat quality was negatively correlated with fertility (-0.312) and growth rate (-0.381). Prolificacy had positive and favourable correlations with drought tolerance (0.603), disease tolerance (0.091) and heat tolerance (0.091). Regarding the preference rank correlation of marketers and consumers, positive and significant correlations were reported for body weight with growth rate (0.092) and meat quality (0.056). IC ecotypes that can perform well and are adaptable to the local environments in South Sudan should be identified. Selections should be based on traits preferred by farmers, marketers, and consumers.

Combined Metabolomic and Quantitative RT-PCR Analyses Revealed the Synthetic Differences of 2-Acetyl-1-pyrroline in Aromatic and Non-Aromatic Vegetable Soybeans

Aroma is an important economic trait of vegetable soybeans, which greatly influences their market value. The 2-acetyl-1-pyrroline (2AP) is considered as an important substance affecting the aroma of plants. Although the 2AP synthesis pathway has been resolved, the differences of the 2AP synthesis in the aromatic and non-aromatic vegetable soybeans are unknown. In this study, a broad targeted metabolome analysis including measurement of metabolites levels and gene expression levels was performed to reveal pathways of aroma formation in the two developmental stages of vegetable soybean grains [35 (S5) and 40 (S6) days after anthesis] of the 'Zhexian No. 8' (ZX8, non-aromatic) and ZK1754 (aromatic). The results showed that the differentially accumulated metabolites (DAMs) of the two varieties can be classified into nine main categories including flavonoids, lipids, amino acids and derivatives, saccharides and alcohols, organic acids, nucleotides and derivatives, phenolic acids, alkaloids and vitamin, which mainly contributed to their phenotypic differences. Furthermore, in combination with the 2AP synthesis pathway, the differences of amino acids and derivatives were mainly involved in the 2AP synthesis. Furthermore, 2AP precursors' analysis revealed that the accumulation of 2AP mainly occurred from 1-pyrroline-5-carboxylate (P5C), not 4-aminobutyraldehyde (GABald). The quantitative RT-PCR showed that the associated synthetic genes were 1-pyrroline-5-carboxylate dehydrogenase (P5CDH), ∆1-pyrroline-5-carboxylate synthetase (P5CS), proline dehydrogenase (PRODH) and pyrroline-5-carboxylate reductase (P5CR), which further verified the synthetic pathway of 2AP. Furthermore, the betaine aldehyde dehydrogenase 2 (GmBADH2) mutant was not only vital for the occurrence of 2AP, but also for the synthesis of 4-aminobutyric acid (GABA) in vegetable soybean. Therefore, the differences of 2AP accumulation in aromatic and non-aromatic vegetable soybeans have been revealed, and it also provides an important theoretical basis for aromatic vegetable soybean breeding.

Identification and characterization of circRNAs related to meat quality during embryonic development of the longissimus dorsi muscle in two pig breeds.

Meat quality, an important economic trait, is regulated by many factors, especially by genetic factors, including coding genes, miRNAs, and lncRNAs. Recent studies have elucidated that circRNAs also play a key role in muscle development and lipid deposition. However, the functions and regulatory mechanisms of circRNAs in meat quality remain mostly unknown. The circRNA expression profiles between Huainan pigs (Chinese indigenous pigs, fat-type, Huainan HN) and Large White pigs (Western commercial pigs, lean-type, LW) in the longissimus dorsi (LD) muscle at 38, 58, and 78days post conception (dpc) were compared by sequencing. In total, 39,887 circRNAs were identified in 18 samples, and 60, 78, and 86 differentially expressed circRNAs (DECs) were found at the three stages mentioned above between these two breeds. The parent genes of DECs were enriched in myogenesis, proliferation, adipogenesis and muscle fiber-type transition. The circRNA-miRNA interaction networks included 38 DECs and 47 miRNAs, and these miRNAs were involved in muscle development and lipid metabolism. Two shared DECs (circ_0030593 and circ_0032760) of these three stages were selected, their head-to-tail junction sites were validated by Sanger sequencing, and RT‒qPCR results suggested that these two DECs might be involved in intramuscular fat deposition. These findings provide a basis for understanding the role of circRNAs in meat quality.

Legume Pangenome: Status and Scope for Crop Improvement.

In the last decade, legume genomics research has seen a paradigm shift due to advances in genome sequencing technologies, assembly algorithms, and computational genomics that enabled the construction of high-quality reference genome assemblies of major legume crops. These advances have certainly facilitated the identification of novel genetic variants underlying the traits of agronomic importance in many legume crops. Furthermore, these robust sequencing technologies have allowed us to study structural variations across the whole genome in multiple individuals and at the species level using 'pangenome analysis.' This review updates the progress of constructing pangenome assemblies for various legume crops and discusses the prospects for these pangenomes and how to harness the information to improve various traits of economic importance through molecular breeding to increase genetic gain in legumes and tackle the increasing global food crisis.

Development and evaluation of liquid SNP array for large yellow croaker (Larimichthys crocea)

In order to promote the genetic selective breeding of large yellow croaker, we designed and developed the liquid single nucleotide polymorphism (SNP) array named NingXin-III that based on the genotyping by target sequencing (GBTS) technology and 55 K high-throughput solid chip-based array (NingXin-II SNP array) of large yellow croaker. NingXin-III SNP array contains 98.85% of the loci on the NingXin-II SNP array, and 1535 new loci, totaling 54,990 loci, which are evenly distributed on 24 chromosomes of large yellow croaker. Based on the NingXin-III SNP array, 89 samples from two batches of large yellow croaker were genotyped, and the results showed that the genotyping success rate of NingXin-III SNP array in both batches was over 97.4%, the average genotype concordant rate of individuals in different batches was 99.56%, and the average genotype concordant rate of duplicate individuals in the same batch was 99.7%. A comparison of the genotyping results of the shared loci on NingXin-II and NingXin-III showed that the average genotype concordant rate of common loci between them reached over 96%. In summary, NingXin-III SNP array has a high genotyping accuracy, high reproducibility and no batch effect, which can completely replace NingXin-II SNP array. NingXin-III SNP array will provide important technical support for genetic improvement of important economic traits of large yellow croaker.

Association analysis of alpha-amylase (AMY) and cathepsin L (CTSL) SNPs with growth traits in giant tiger shrimp Penaeus monodon

Alpha-amylase (AMY) and cathepsin-L (CTSL) were selected as candidate genes for SNP discovery for growth traits of P. monodon. Six SNPs were found in AMY and three in CTSL in P. monodon. Association analyses for the candidate SNPs with important economic traits were performed in populations. That allele A at CTLS-213 SNP, AA, and GA, tended to be associated with increased body weight. Shrimps with genotype GG had significantly smaller CL, CW, and CH values than those with GT and TT genotypes (P < 0.05). While CTLS-820 SNP was found to be significantly associated with CH and FSL (P <0.05). These SNPs will be valid for marker-assisted selection breeding programs in P. monodon.

Volatiles and Transcriptome Profiling Revealed the Formation of ‘Taro-like’ Aroma in the Leaf of Pumpkin (Cucurbita moschata)

‘Taro-like’ odor is an important economic trait of pumpkin species. The metabolic and molecular bases of this aromatic trait remain largely unexplored. Therefore, in this study, gas chromatography-mass spectrometry, GC-Olfactometry, and RNA-seq technology were used to illuminate the differential volatile compounds, the key volatile compounds, and differentially expressed genes (DEGs) in leaves from two pumpkin samples. Eight volatile compounds, including (E)-2-nonenal, 3-octanol, 2-ethyl-1-hexanol, 1-nonanol, α-terpineol, 2,3-pentanedione, caryophyllene, and 2-acetyl-1-pyrroline, were only detected in the sample with ‘taro-like’ aroma. Moreover, the variable importance in projection scores of all the above eight volatile compounds were >1.0 using PLS-DA analysis. The compounds 2-acetyl-1-pyrroline, 3-octanol, 1-nonanol, and (E)-3,7-dimethyl-2,6-octadienal were identified as the key contributors using GC-Olfactometry analysis. It was determined that 2-acetyl-1-pyrroline might play a significant role in ‘taro-like’ aroma. Furthermore, most of the differential volatile compounds were derived from fatty acids, and the DEGs were also involved in the pathways related to degradation, metabolism, and biosynthesis of fatty acids. Moreover, five genes involved in the accumulation of 2-acetyl-1-pyrroline showed differential expression, and their expression trends were consistent with 2-acetyl-1-pyrroline. This study offers the basis for further studies on the mechanism of ‘taro-like’ aroma in pumpkins.

Selection parameters for improving grain yield of bread wheat under terminal heat stress

Improving terminal heat tolerance is an issue of top priority in wheat breeding in the present era of climate change. Present study was carried out to identify the association among traits of economic importance under terminal heat stress environment. The grain yield/sq. meter under terminal heat stress environment recorded highly significant positive correlation both at genotypic and phenotypic level with grain weight/spike, number of spike/sq. meter, harvest index and 1000-grain weight in both the crop seasons. Path coefficient analysis carried out using genotypic correlation coefficients revealed that days to heading contributing maximum positive direct effect towards grain yield under terminal heat stress environment followed by grain filling duration. Other characters contributing positive direct effects towards grain yield were grain weight/spike, number of spike/sq. meter, harvest index and biological yield/sq. meter under both the crop season. Thus, for improving the wheat grain yield under terminal heat stresses conditions, breeder should aim for selecting genotypes with bold grains or high grain weight /spike, more number of tillers/sq. meter, higher harvest index and longer grain filling duration.

Integration of ATAC-seq and RNA-seq analysis identifies key genes affecting intramuscular fat content in pigs.

Meat quality is one of the most important economic traits in pig breeding and production, and intramuscular fat (IMF) content is the major factor in improving meat quality. The IMF deposition in pigs is influenced by transcriptional regulation, which is dependent on chromatin accessibility. However, how chromatin accessibility plays a regulatory role in IMF deposition in pigs has not been reported. Xidu black is a composite pig breed with excellent meat quality, which is an ideal research object of this study. In this study, we used the assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) analysis to identify the accessible chromatin regions and key genes affecting IMF content in Xidu black pig breed with extremely high and low IMF content. First, we identified 21,960 differential accessible chromatin peaks and 297 differentially expressed genes. The motif analysis of differential peaks revealed several potential cis-regulatory elements containing binding sites for transcription factors with potential roles in fat deposition, including Mef2c, CEBP, Fra1, and AP-1. Then, by integrating the ATAC-seq and RNA-seq analysis results, we found 47 genes in the extremely high IMF (IMF_H) group compared with the extremely low IMF (IMF_L) group. For these genes, we observed a significant positive correlation between the differential gene expression and differential ATAC-seq signal (r2 = 0.42). This suggests a causative relationship between chromatin remodeling and the resulting gene expression. We identified several candidate genes (PVALB, THRSP, HOXA9, EEPD1, HOXA10, and PDE4B) that might be associated with fat deposition. Through the PPI analysis, we found that PVALB gene was the top hub gene. In addition, some pathways that might regulate fat cell differentiation and lipid metabolism, such as the PI3K-Akt signaling pathway, MAPK signaling pathway, and calcium signaling pathway, were significantly enriched in the ATAC-seq and RNA-seq analysis. To the best of our knowledge, our study is the first to use ATAC-seq and RNA-seq to examine the mechanism of IMF deposition from a new perspective. Our results provide valuable information for understanding the regulation mechanism of IMF deposition and an important foundation for improving the quality of pork.

Comparative analysis of mitochondrial genomes of maize CMS-S subtypes provides new insights into male sterility stability

BackgroundCytoplasmic male sterility (CMS) is a trait of economic importance in the production of hybrid seeds. In CMS-S maize, exerted anthers appear frequently in florets of field-grown female populations where only complete male-sterile plants were expected. It has been reported that these reversions are associated with the loss of sterility-conferring regions or other rearrangements in the mitochondrial genome. However, the relationship between mitochondrial function and sterility stability is largely unknown.ResultsIn this study, we determined the ratio of plants carrying exerted anthers in the population of two CMS-S subtypes. The subtype with a high ratio of exerted anthers was designated as CMS-Sa, and the other with low ratio was designated as CMS-Sb. Through next-generation sequencing, we assembled and compared mitochondrial genomes of two CMS-S subtypes. Phylogenetic analyses revealed strong similarities between the two mitochondrial genomes. The sterility-associated regions, S plasmids, and terminal inverted repeats (TIRs) were intact in both genomes. The two subtypes maintained high transcript levels of the sterility gene orf355 in anther tissue. Most of the functional genes/proteins were identical at the nucleotide sequence and amino acid sequence levels in the two subtypes, except for NADH dehydrogenase subunit 1 (nad1). In the mitochondrial genome of CMS-Sb, a 3.3-kilobase sequence containing nad1-exon1 was absent from the second copy of the 17-kb repeat region. Consequently, we detected two copies of nad1-exon1 in CMS-Sa, but only one copy in CMS-Sb. During pollen development, nad1 transcription and mitochondrial biogenesis were induced in anthers of CMS-Sa, but not in those of CMS-Sb. We suggest that the impaired mitochondrial function in the anthers of CMS-Sb is associated with its more stable sterility.ConclusionsComprehensive analyses revealed diversity in terms of the copy number of the mitochondrial gene nad1-exon1 between two subtypes of CMS-S maize. This difference in copy number affected the transcript levels of nad1 and mitochondrial biogenesis in anther tissue, and affected the reversion rate of CMS-S maize. The results of this study suggest the involvement of mitochondrial robustness in modulation of sterility stability in CMS-S maize.

Identification of Signatures of Selection for Litter Size and Pubertal Initiation in Two Sheep Populations.

Simple SummaryFecundity is an important economic trait of sheep that directly affects their economic and productive efficiency. Our study aimed to identify single nucleotide polymorphism (SNP) loci associated with sheep puberty or litter size which could be used in future breeding programs to improve fertility. We obtained one SNP on GNAQ gene (NC_040253.1: g.62677376G > A), which was associated with litter size in Cele Black sheep. Perhaps this SNP could be a criterion to screen polytocous sheep.Fecundity is an important economic trait in sheep that directly affects their economic and productive efficiency. Our study aimed to identify SNP loci associated with sheep puberty or litter size which could be used in future breeding programs to improve fertility. Genomic DNA was obtained from Hetian and Cele Black sheep breeds and used for reduced-representation genome sequencing to identify SNP loci associated with pubertal initiation and litter size. Selective signatures analysis was performed based on the fixation index and nucleotide diversity, followed by pathway analysis of the genes contained in the selected regions. The selected SNP loci in the genes associated with pubertal initiation and litter size were validated using both sheep breeds. In total, 384,718 high quality SNPs were obtained and 376 genes were selected. Functional annotation of genes and enrichment analysis identified 12 genes associated with pubertal initiation and 11 genes associated with litter size. SNP locus validation showed that two SNP on PAK1 and four on ADCY1 may be associated with pubertal initiation, and one SNP on GNAQ gene (NC_040253.1: g.62677376G > A) was associated with litter size in Cele Black sheep. Our results provide new theoretical support for sheep breeding.

WheatQTLdb V2.0: a supplement to the database for wheat QTL.

We recently developed a database for hexaploid wheat QTL (WheatQTLdb; www.wheatqtldb.net), which included 11,552 QTL affecting various traits of economic importance. However, that database did not include valuable QTL from other wheat species and/or progenitors of hexaploidwheat. Therefore, an updated and improved version of wheat QTL database (WheatQTLdb V2.0) was developed, which now includes information on hexaploid wheat (Triticum aestivum) and the following seven other related species: T. durum, T. turgidum, T. dicoccoides, T. dicoccum, T. monococcum, T. boeoticum, and Aegilops tauschii. WheatQTLdb V2.0 includes a much-improved list of QTL, including 27,518 main effect QTL, 202 epistatic QTL, and 1321 metaQTL. This newly released WheatQTLdb V2.0 also has additional valuable options to search and choose the QTL, category-wise, and trait-wise data for their use inresearch or breeding programs.

Model Comparison of Heritability Enrichment Analysis in Livestock Population.

Heritability enrichment analysis is an important means of exploring the genetic architecture of complex traits in human genetics. Heritability enrichment is typically defined as the proportion of an SNP subset explained heritability, divided by the proportion of SNPs. Heritability enrichment enables better study of underlying complex traits, such as functional variant/gene subsets, biological networks and metabolic pathways detected through integrating explosively increased omics data. This would be beneficial for genomic prediction of disease risk in humans and genetic values estimation of important economical traits in livestock and plant species. However, in livestock, factors affecting the heritability enrichment estimation of complex traits have not been examined. Previous studies on humans reported that the frequencies, effect sizes, and levels of linkage disequilibrium (LD) of underlying causal variants (CVs) would affect the heritability enrichment estimation. Therefore, the distribution of heritability across the genome should be fully considered to obtain the unbiased estimation of heritability enrichment. To explore the performance of different heritability enrichment models in livestock populations, we used the VanRaden, GCTA and α models, assuming different α values, and the LDAK model, considering LD weight. We simulated three types of phenotypes, with CVs from various minor allele frequency (MAF) ranges: genome-wide (0.005 ≤ MAF ≤ 0.5), common (0.05 ≤ MAF ≤ 0.5), and uncommon (0.01 ≤ MAF < 0.05). The performances of the models with two different subsets (one of which contained known CVs and the other consisting of randomly selected markers) were compared to verify the accuracy of heritability enrichment estimation of functional variant sets. Our results showed that models with known CV subsets provided more robust enrichment estimation. Models with different α values tended to provide stable and accurate estimates for common and genome-wide CVs (relative deviation 0.5–2.2%), while tending to underestimate the enrichment of uncommon CVs. As the α value increased, enrichments from 15.73% higher than true value (i.e., 3.00) to 48.93% lower than true value for uncommon CVs were observed. In addition, the long-range LD windows (e.g., 5000 kb) led to large bias of the enrichment estimations for both common and uncommon CVs. Overall, heritability enrichment estimations were sensitive for the α value assumption and LD weight consideration of different models. Accuracy would be greatly improved by using a suitable model. This study would be helpful in understanding the genetic architecture of complex traits and provides a reference for genetic analysis in the livestock population.

Characterization of a foxtail mosaic virus vector for gene silencing and analysis of innate immune responses in Sorghum bicolor.

Sorghum is vulnerable to many biotic and abiotic stresses, which cause considerable yield losses globally. Efforts to genetically characterize beneficial sorghum traits, including disease resistance, plant architecture, and tolerance to abiotic stresses, are ongoing. One challenge faced by sorghum researchers is its recalcitrance to transformation, which has slowed gene validation efforts and utilization for cultivar development. Here, we characterize the use of a foxtail mosaic virus (FoMV) vector for virus-induced gene silencing (VIGS) by targeting two previously tested marker genes: phytoene desaturase (PDS) and ubiquitin (Ub). We additionally demonstrate VIGS of a subgroup of receptor-like cytoplasmic kinases (RLCKs) and report the role of these genes as positive regulators of early defence signalling. Silencing of subgroup 8 RLCKs also resulted in higher susceptibility to the bacterial pathogens Pseudomonas syringae pv. syringae (B728a) and Xanthomonas vasicola pv. holcicola, demonstrating the role of these genes in host defence against bacterial pathogens. Together, this work highlights the utility of FoMV-induced gene silencing in the characterization of genes mediating defence responses in sorghum. Moreover, FoMV was able to systemically infect six diverse sorghum genotypes with high efficiency at optimal temperatures for sorghum growth and therefore could be extrapolated to study additional traits of economic importance.

Estimation of genetic correlations of two key feed efficiency traits with production traits in male Hu sheep

Increased body growth and feed efficiency are important for breeding due to expensive feed costs. This study estimated the genetic parameters for two feed efficiency traits [the feed conversion ratio (FCR) and the residual feed intake (RFI)] and other important economic traits in male Hu sheep using 1642 male Hu lambs. The heritability of the RFI was estimated at 0.31 (±0.10)–0.54 (±0.1) and the heritability of the FCR was 0.05 (±0.07)–0.77 (±0.12). There was a negative genetic correlation between rib-eye muscle area traits and RFI. A positive genetic correlation was found between fat deposition traits and feed efficiency traits. The digestive tract weight decreased with the direction of RFI: however, the FCR showed the opposite: A low FCR was accompanied by a high digestive tract weight. The genetic correlation between feed efficiency (RFI and FCR) and rumen weight was negative. Heritability estimates for feed efficiency generate fluctuations with different experimental intervals. The weight of other traits should be reasonably allocated to avoid losses in production and feed efficiency in the selection of feed efficiency traits. The present study added to our understanding of the genetic parameters of sheep under the condition of house feeding.

Identifying selection signatures for litter size in Guangxi Bama Xiang pigs.

Litter size is an important economic trait in pig production. However, the genetic mechanisms underlying varying litter size in Guangxi Bama Xiang pigs remain unknown. To identify selection signatures for litter size in Guangxi Bama Xiang pigs, we obtained 297 Illumina PorcineSNP50 BeadChip array data and the average born number (ABN) from parity one to nine in Guangxi Bama Xiang pigs. Fixation index (Fst) methods were used to identify the selection signature of the litter size, and three phenotypic gradient differential population pairs (according to the ABN) in individuals were used to reduce the false positives of signature selections. Single nucleotide polymorphisms (SNPs) were identified in the VEGFA promoter and exons. The general linear model was used to analyse the differences in distinct genotypes after they were typed using three-round multiplex PCR technology. Finally, the transcriptome factor and CpG island in the VEGFA promoter were predicted. A total of 328, 328 and 317 significant loci were identified in the 1st, 2nd and 3rd population pairs, respectively. After removing the false positives, 25 SNPs were defined as the selection signatures in relation to litter size. Ten (VEGFA, USP49, USP25, SRPK1, SLC26A8, RPL10A, PPARD, MAPK14, HMGA1 and CHRDL2) out of 52 genes in the selection regions were annotated as the candidate genes of litter size, respectively, VEGFA. There were no SNPs in the VEGFA exon region, but we obtained three SNPs (rs786889605, rs343769603 and rs323942424) in the VEGFA promoter regions. The ABN in CC was significantly higher than that in TT in rs786889605, and the ABN in TT was significantly lower than that in GG in rs323942424. Meanwhile, the mutation of the VEGFA promoter result in the loss of Sp1 and NF-1 and the formation of Oct-1. In summary, we obtained ten candidate genes, and two mutations in the VEGFA promoter that could be important potential molecular biomarkers for litter size in Bama Xiang pigs.

Additive genetic variation in resistance of Nile tilapia (Oreochromis niloticus) to Francisella orientalis and its genetic (co)variation to both harvest weight and resistance to Streptococcus agalactiae Ib

An understanding of the genetic relationship between traits of economic importance for a widely cultured species such as Nile tilapia (Oreochromis niloticus) is important, in particular the relationship between disease resistance and growth. Francisellosis results in economic losses for the industry, and we confirmed that Francisellosis resistance is under additive genetic control in our population. Analysing four generations, significant additive genetic variation was found for survival to F. orientalis challenge (P < 0.001; Log-likelihood-ratio test) with an estimated heritability of h2 = 0.31 ± 0.05 across all generations. The random effect common to full-sibs was also significant, but of lower magnitude (c2 = 0.075 ± 0.02) (P < 0.001; Log-likelihood-ratio test). Results of assortative mating groups confirmed that genetic gain could be obtained for survival to F. orientalis challenge since offspring of fish selected with high estimated breeding values exhibited higher survival to F. orientalis challenge. The genetic correlation between harvest weight and survival to F. orientalis challenge was very low (rg = −0.02 ± 0.13) and not significantly different from zero (Log-likelihood-ratio test p > 0.05). The genetic correlation between survival to F. orientalis challenge and survival to S. agalactiae Ib challenge was positive but not significantly different from zero (rg = 0.14 ± 0.11; Log-likelihood-ratio test p > 0.05). The genetic correlation between harvest weight and survival to S. agalactiae challenge was negative but also not significantly different (rg = − 0.19 ± 0.10; Log-likelihood-ratio test p > 0.05). Lack of significant favourable genetic relationships between economically important traits favours multi-trait selection since selection for growth alone does not improve survival to F. orientalis challenge or survival to S. agalactiae challenge.

Meta-analysis of association between c.963A>G single-nucleotide polymorphism on BMP15 gene and litter size in goats.

Litter size is an important economic trait in the goat industry. Previous studies on the bone morphogenetic protein15 (BMP15) gene detected some single-nucleotide polymorphisms (SNPs) such as c.963A G that were associated with an increase in ovulation rate and litter size. The aim of this study was to conduct a meta-analysis on the effect of this polymorphism on litter size. We gathered and pooled data from five eligible published studies. To investigate the effect of c.963A G on litter size, we utilized four different genetic models assuming dominant (GG GA vs. AA), recessive (GG vs. GA AA), additive (GG vs. AA) and co-dominant (GG AA vs. GA) model of inheritance. Data were analyzed under random-effects models based on the value. Furthermore, sensitivity analysis was carried out to validate the stability of results. The results showed that the c.963A G polymorphism is associated with litter size when applying a dominant model (standardized mean difference (SMD) is 0.815, 95 % CI[0.170, 1.461], value 0.013) and also with an additive model (SMD 0.755, 95 % CI[0.111, 1.400], value 0.022). However, the effect of c.963A G polymorphism was not significant under recessive (SMD 0.186, 95 % CI[ 0.195, 4.259], value 0.339) and co-dominant (SMD 0.119, 95 % CI[ 0.525, 0.288], value 0.568) models. Sensitivity analysis demonstrated that dropping studies with wide confidence intervals affects overall results under the assumption of an additive model. The meta-analysis results revealed that the AA genotype could be positively connected with litter size in goats.