• Asian-Australasian Journal of Animal Sciences
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• v.28 no.4
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• pp.467-475
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• 2015

Improvement for carcass traits related to beef quality is the key concern in beef production. Recent reports found that epigenetics mediates the interaction of individuals with environment and nutrition. The present study was designed to analyze the genetic effect of single nucleotide polymorphisms (SNPs) in seven epigenetic-related genes (DNMT1, DNMT3a, DNMT3b, DNMT3L, Ago1, Ago2, and HDAC5) and two meat quality candidate genes (CAPN1 and PRKAG3) on fourteen carcass traits related to beef quality in a Snow Dragon beef population, and also to identify SNPs in a total of fourteen cattle populations. Sixteen SNPs were identified and genotyped in 383 individuals sampled from the 14 cattle breeds, which included 147 samples from the Snow Dragon beef population. Data analysis showed significant association of 8 SNPs within 4 genes related to carcass and/or meat quality traits in the beef populations. SNP1 (13154420A>G) in exon 17 of DNMT1 was significantly associated with rib-eye width and lean meat color score (p<0.05). A novel SNP (SNP4, 76198537A>G) of DNMT3a was significantly associated with six beef quality traits. Those individuals with the wild-type genotype AA of DNMT3a showed an increase in carcass weight, chilled carcass weight, flank thicknesses, chuck short rib thickness, chuck short rib score and in chuck flap weight in contrast to the GG genotype. Five out of six SNPs in DNMT3b gene were significantly associated with three beef quality traits. SNP15 (45219258C>T) in CAPN1 was significantly associated with chuck short rib thickness and lean meat color score (p<0.05). The significant effect of SNP15 on lean meat color score individually and in combination with each of other 14 SNPs qualify this SNP to be used as potential marker for improving the trait. In addition, the frequencies of most wild-type alleles were higher than those of the mutant alleles in the native and foreign cattle breeds. Seven SNPs were identified in the epigenetic-related genes. The SNP15 in CAPN1 could be used as a powerful genetic marker in selection programs for beef quality improvement in the Snow Dragon Beef population.

• International Journal of Industrial Entomology and Biomaterials
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• v.13 no.1
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• pp.15-22
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• 2006

An experiment was conducted to study the efficiency of cyanobacterial biofertilizer (CBB) with chemical (NPK) fertilizer on quantitative and qualitative characters of mulberry variety Kanva-2. Their influences on silkworm growth and cocoon characters were also studied. Ten different CBB and NPK fertilizer treatments were given to 5000 plants of established mulberry garden. Treatments were of four types viz., (i) T1 to T7: single and combination dose of CBB+50% NPK (ii) T8: combination dose of CBB + 25%NPK, (iii) T9: CBB only and (iv) T10: control-l00% NPK. Soil pH decreased and nutrients status increased in CBB (T1- T9) treated plots. Average of ten crops data on quantitative traits revealed that T7 (CBB [N. muscorum (1.0 g), A. variahilis (1.0) and S. millei (1.0 g)] + 50% NPK) was very effective in improving growth parameters. Leaf yield was also found high in treatment T7 (32.12 tons/ha/yr.) followed by T10 (31.17 tons/ha/yr.) and T8 (27.67 tons/ha/yr.). Leaf quality characters were found high in T7 and low in T9. Most of the quality traits in T7 are on par with control no. The results revealed that reduction in the dose of chemical fertilizers in T7 did not affect the leaf yield and leaf quality traits of mulberry. This clearly indicates that the efficiency of CBB (T7) provides nitrogen, increases essential nutrients available in soil, maintain soil pH and supply growth substances required for the improvement of leaf yield and leaf quality of mulberry. Bioassay study also revealed no significant difference in silkworm growth and cocoon characters between treatments T7 and T10. Economics calculated revealed that T7 is highly economical and beneficial over T10 by gaining an amount of Rs. 660/-/acre/crop. Thus, treatment T7 containing N. muscorum (1.0 g), A. variahilis (1.0 g) and S. millei (1.0 g) + 50% NPK fertilizers can be recommended to sericulturists mainly to reduce the use of NPK fertilizers, by saving 50% of its cost and to improve soil fertility conditions, which in turn improves leaf yield and quality of mulberry.

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.11
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• pp.1405-1411
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• 2010

Calpastatin (CAST), an endogenous inhibitor of the calpains, plays an important role in post-mortem tenderization of meat. The objectives of this study were to investigate single nucleotide polymorphisms (SNPs) in the bovine CAST gene and association with carcass and meat quality traits. A total of 212 cattle from commercial herds were tested in this study including 2 pure introduced breeds, 4 cross populations, and 3 pure Chinese native breeds. Five SNPs were identified at position 2959 (A/G), 2870 (G/A), 3088 (C/T), 3029 (G/A) and 2857 (C/T) in the CAST gene (GenBank Accession No. AF159246). Allele frequencies of SNP2959 and SNP2870 were 0.701 (A) and 0.462 (A), respectively. A general linear model was used to evaluate the associations between the two markers and 7 traits. The results showed that both SNP2959 and SNP2870 were significantly (p<0.01) associated with the Warner-Bratzler shear force (WBSF), while they had no significant association with the other 6 traits in the whole population. However, in Chinese native pure breeds, only SNP2870 had significant association with WBSF (p<0.05). The simultaneous analysis of two-marker genotype effects indicated animals containing the A/G haplotype (A for SNP2959 and G for SNP2870) tended to have lower shear force than those containing the G/A haplotype, and, especially, animals homozygous for the A/G haplotype had approximately 2 kg lower shear force than those homozygous for the G/A haplotype (p<0.01). These results suggested that both markers may be effective for the marker-assisted selection of meat quality traits in Chinese commercial herds, especially SNP2870 which can be used for Chinese native cattle.

• Journal of Animal Science and Technology
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• v.65 no.5
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• pp.1081-1093
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• 2023

This study aimed to compare meat quality traits between Berkshire and crossbreed (Landrace × Yorkshire × Duroc), and to investigate the relationship between meat quality traits and fatty acid composition. 20 Berkshire and 20 crossbreed pigs were used to compare pork loin quality and to determine the relationship between measured variables. 23 variables were measured including proximate composition, pH, drip loss and cooking loss, Warner-Bratzler shear force, and fatty acid composition. Berkshire had higher moisture content, pH, water-holding capacity, saturated fatty acids, and redness than the crossbreed pig (p < 0.05). The fat content and polyunsaturated fatty acid were low (p < 0.05) in Berkshire. Correlation analysis showed a negatively correlation between moisture and fat content, and a positively correlation between saturated fatty acid and fat content. Moreover, saturated fatty acid and polyunsaturated fatty acid were negatively correlated. As a result of factor analysis and partial least square regression, saturated fatty acid and polyunsaturated fatty acid were estimated to be the main factors affecting quality characteristics of pork. Pig breed is associated with differences in meat quality, and fatty acid composition can have an effect on meat quality parameters.

• Korean Journal of Poultry Science
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• v.42 no.4
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• pp.315-325
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• 2015

Recently, livestock breeding is more focused on the meat quality rather than meat quantity, mainly due to the improvement of consumers' income. Among the meat quality traits, meat color is one of very important traits because meat color is the first selection criterion from the consumers in the market. Most of the economically important traits have continuous variations and these are called quantitative traits. the genomic locations affecting these traits are called quantitative trait locus (QTL), which is mostly controlled by many genes having small effects. In this study, the recent QTL and candidate gene studies were reviewed in order to meet the consumers' demand for the future market. In the chicken QTL database, three traits are related with meat colors, namely breast color (Bco), meat color (Mco), drip loss (DL) and pH. The identified number of QTLs is 33 from 13 chromosomal regions. In these QTL regions, 14 candidate genes were identified; Eight for meat color (APP, BCMO1, COL1A2, FTO, KPNA2, PSMD12, G0S2, FTSJ3), two for drip loss (AGRP, FTO) and four for pH (GALNT1, PCDH19, DIAPH1, SPP2). These QTLs and candidate genes need to be confirmed and fine mapping is ultimately needed for identification of causative variations. The recently developed chicken resource population using Korean native chicken can be used for the improvement of meat quality traits, which increase the value that needed in the chicken industry.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.5
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• pp.611-616
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• 2006

Genetic parameters for performance traits on 409 bulls and growth and carcass traits on 591 of their steer progeny were estimated in Japanese Black cattle with Gibbs sampling. Traits of bulls included body weight at the start (BWS) and finish (BWF) of test, daily gain (DG), concentrate, roughage and TDN intake, and TDN conversion ratio. Progeny traits were BWS, BWF, DG, rib eye area, marbling score (MSR), dressing percentage and subcutaneous fat thickness (SFT). In bulls, heritabilities were high for BWS (0.50) and BWF (0.63) and moderate for concentrate (0.48) and TDN intake (0.45), while in progeny, the heritability for all the studied traits was moderate to high (ranging from 0.30 to 0.73), highlighting the potential for genetic improvement of these traits. Genetic correlations between TDN intake and growth traits (BWS, BWF and DG) in bulls were highly positive (ranging from 0.77 to 0.94). The weak but negative genetic correlation (-0.20) between MSR and SFT in progeny indicated that improvement of beef marbling without increasing subcutaneous fat deposition could be possible. The estimated genetic correlations of roughage intake of bulls with body weights (BWS and BWF) and MSR of their progeny were moderate (ranging from 0.35 to 0.52). On the basis of the selection for bulls, growth traits and TDN intake correlated positively with SFT (ranging from 0.43 to 0.53) of their progeny, suggesting the necessity of controlling the increase of SFT in selection programs.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.10
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• pp.1529-1534
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• 2008

The aim of this study was directed at exploring the possible use of muscle fiber characteristics as new selection traits for improving both porcine lean meat production and quality. A total of 174 (114 Yorkshire, 30 Landrace, and 30 Meishan) pigs were used for this study, and lean meat production ability was estimated by backfat thickness and loin eye area. The Longissimus dorsi muscle was taken in order to measure meat quality and muscle fiber characteristics. Due to the high correlations between total muscle fiber number and most of the performance traits, all pigs were classified into three groups (low, intermediate, or high) by total muscle fiber number using cluster analysis. The high group had the highest loin eye area (p<0.001). The meat quality traits were within normal ranges as reddish pink, firm, and nonexudative (RFN) pork, but the groups classified as intermediate and high had relatively large drip loss percentages (p<0.05), produced more than twice the amount of pale, soft, and exudative (PSE) pork as compared to the low group. The group with a high total muscle fiber number was further classified, based on type 2b fiber percentage, into low or high groups by cluster analysis. The results showed that the low type 2b fiber group had good loin eye area (p<0.05), small drip loss (p<0.05), and did not produce PSE pork. For these reasons, a high total muscle fiber number, with a low percentage of type 2b fibers, may be suitable in selecting for improvements in both lean meat production and meat quality.

• Proceedings of the Korean Society of Near Infrared Spectroscopy Conference
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• 2001.06a
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• pp.1618-1618
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• 2001

Predicting quality traits using near infrared (NIR) spectroscopy on whole grain samples has gained wide acceptance as a non-destructive, rapid and cost effective technique. Barley breeding programs throughout southern Australia currently use this technology as a tool for selecting malting quality lines. For the past 3 years whole grain barley calibrations have been developed at VIDA to predict malting quality traits in the early generation selections of the breeding program. More recently calibrations for whole grain malt have been developed and introduced to aid in selecting malted samples at the mid-generation stage for more complex malting quality traits. Using the same population set, barley and malt calibrations were developed to predict hot water extracts (EBC and IoB), diastatic power, free $\alpha$-amino nitrogen, soluble protein, wort $\beta$-glucan and $\beta$-glucanase. The correlation coefficients between NIR predicted values and laboratory methods for malt were all highly significant ($R^2$ > 0.84), whereas the correlation coefficients for the barley calibrations were lower ($R^2$ > 0.57) but still significant. The magnitude of the error in predicting hot water extract, diastatic power and wort $\beta$-glucan using whole grain malt was reduced by 50% when compared with predicting the same trait using whole grain barley. This can be explained by the complex nature of attempting to develop calibrations on whole grain barley utilizing malt data. During malting, the composition of barley is modified by the action of enzymes throughout the steeping and germination stages and by heating during the kilning stage. Predicting malting quality on whole grain malt is a more reliable alternative to predicting whole grain barley, although there is the added expense of micro-malting the samples. The ability to apply barley and malt calibrations to different generations is an advantage to a barley breeding program that requires thousands of samples to be assessed each year.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.10
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• pp.1535-1541
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• 2018

Objective: In birds, three types of melatonin receptors (MTNR1A, MTNR1B, and MTNR1C) have been cloned. Previous researches have showed that three melatonin receptors played an essential role in reproduction and ovarian physiology. However, the association of polymorphisms of the three receptors with duck reproduction traits and egg quality traits is still unknown. In this test, we chose MTNR1A, MTNR1B, and MTNR1C as candidate genes to detect novel sequence polymorphism and analyze their association with egg production traits in Shaoxing duck, and detected their mRNA expression level in ovaries. Methods: In this study, a total of 785 duck blood samples were collected to investigate the association of melatonin receptor genes with egg production traits and egg quality traits using a direct sequencing method. And 6 ducks representing two groups (3 of each) according to the age at first eggs (at 128 days of age or after 150 days of age) were carefully selected for quantitative real-time polymerase chain reaction. Results: Seven novel polymorphisms (MTNR1A: g. 268C>T, MTNR1B: g. 41C>T, and g. 161T>C, MTNR1C: g. 10C>T, g. 24A>G, g. 108C>T, g. 363 T>C) were detected. The single nucleotide polymorphism (SNP) of MTNR1A (g. 268C>T) was significantly linked with the age at first egg (p<0.05). And a statistically significant association (p<0.05) was found between MTNR1C g.108 C>T and egg production traits: total egg numbers at 34 weeks old of age and age at first egg. In addition, the mRNA expression level of MTNR1A in ovary was significantly higher in late-mature group than in early-mature group, while MTNR1C showed a contrary tendency (p<0.05). Conclusion: These results suggest that identified SNPs in MTNR1A and MTNR1C may influence the age at first egg and could be considered as the candidate molecular marker for identify early maturely traits in duck selection and improvement.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.207-207
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• 2022

Eating and cooking quality (ECQ) is one of the most complex quantitative traits in rice. The understanding of genetic regulation of transcript expression levels attributing to phenotypic variation in ECQ traits is limited. We integrated whole-genome resequencing, transcriptome, and phenotypic variation data from 84 Japonica accessions to build a transcriptome-wide association study (TWAS) based regulatory network. All ECQ traits showed a large phenotypic variation and significant phenotypic correlations among the traits. TWAS analysis identified a total of 285 transcripts significantly associated with six ECQ traits. Genome-wide mapping of ECQ-associated transcripts revealed 66,905 quantitative expression traits (eQTLs), including 21,747 local eQTLs, and 45,158 trans-eQTLs, regulating the expression of 43 genes. The starch synthesis-related genes (SSRGs), starch synthase IV-1 (SSIV-1), starch branching enzyme 1 (SBE1), granule-bound starch synthase 2 (GBSS2), and ADP-glucose pyrophosphorylase small subunit 2a (OsAGPS2a) were found to have eQTLs regulating the expression of ECQ associated transcripts. Further, in co-expression analysis, 130 genes produced at least one network with 22 master regulators. In addition, we developed CRISPR/Cas9-edited glbl mutant lines that confirmed the role of alpha-globulin (glbl) in starch synthesis to validate the co-expression analysis. This study provided novel insights into the genetic regulation of ECQ traits, and transcripts associated with these traits were discovered that could be used in further rice breeding.