• Asian-Australasian Journal of Animal Sciences
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• 제32권9호
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• pp.1340-1348
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• 2019

Objective: The objectives were to compare variance components, genetic parameters, prediction accuracies, and genomic-polygenic estimated breeding value (EBV) rankings for milk yield (MY) and fat yield (FY) in the Thai multibreed dairy population using five single nucleotide polymorphism (SNP) sets from GeneSeek GGP80K chip. Methods: The dataset contained monthly MY and FY of 8,361 first-lactation cows from 810 farms. Variance components, genetic parameters, and EBV for five SNP sets from the GeneSeek GGP80K chip were obtained using a 2-trait single-step average-information restricted maximum likelihood procedure. The SNP sets were the complete SNP set (all available SNP; SNP100), top 75% set (SNP75), top 50% set (SNP50), top 25% set (SNP25), and top 5% set (SNP5). The 2-trait models included herd-year-season, heterozygosity and age at first calving as fixed effects, and animal additive genetic and residual as random effects. Results: The estimates of additive genetic variances for MY and FY from SNP subsets were mostly higher than those of the complete set. The SNP25 MY and FY heritability estimates (0.276 and 0.183) were higher than those from SNP75 (0.265 and 0.168), SNP50 (0.275 and 0.179), SNP5 (0.231 and 0.169), and SNP100 (0.251and 0.159). The SNP25 EBV accuracies for MY and FY (39.76% and 33.82%) were higher than for SNP75 (35.01% and 32.60%), SNP50 (39.64% and 33.38%), SNP5 (38.61% and 29.70%), and SNP100 (34.43% and 31.61%). All rank correlations between SNP100 and SNP subsets were above 0.98 for both traits, except for SNP100 and SNP5 (0.93 for MY; 0.92 for FY). Conclusion: The high SNP25 estimates of genetic variances, heritabilities, EBV accuracies, and rank correlations between SNP100 and SNP25 for MY and FY indicated that genotyping animals with SNP25 dedicated chip would be a suitable to maintain genotyping costs low while speeding up genetic progress for MY and FY in the Thai dairy population.

• Journal of Animal Science and Technology
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• 제65권4호
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• pp.720-734
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• 2023

In Korea, Korea Proven Bulls (KPN) program has been well-developed. Breeding and evaluation of cows are also an essential factor to increase earnings and genetic gain. This study aimed to evaluate the accuracy of cow breeding value by using three methods (pedigree index [PI], pedigree-based best linear unbiased prediction [PBLUP], and genomic-BLUP [GBLUP]). The reference population (n = 16,971) was used to estimate breeding values for 481 females as a test population. The accuracy of GBLUP was 0.63, 0.66, 0.62 and 0.63 for carcass weight (CWT), eye muscle area (EMA), back-fat thickness (BFT), and marbling score (MS), respectively. As for the PBLUP method, accuracy of prediction was 0.43 for CWT, 0.45 for EMA, 0.43 for MS, and 0.44 for BFT. Accuracy of PI method was the lowest (0.28 to 0.29 for carcass traits). The increase by approximate 20% in accuracy of GBLUP method than other methods could be because genomic information may explain Mendelian sampling error that pedigree information cannot detect. Bias can cause reducing accuracy of estimated breeding value (EBV) for selected animals. Regression coefficient between true breeding value (TBV) and GBLUP EBV, PBLUP EBV, and PI EBV were 0.78, 0.625, and 0.35, respectively for CWT. This showed that genomic EBV (GEBV) is less biased than PBLUP and PI EBV in this study. In addition, number of effective chromosome segments (M_e) statistic that indicates the independent loci is one of the important factors affecting the accuracy of BLUP. The correlation between M_e and the accuracy of GBLUP is related to the genetic relationship between reference and test population. The correlations between M_e and accuracy were -0.74 in CWT, -0.75 in EMA, -0.73 in MS, and -0.75 in BF, which were strongly negative. These results proved that the estimation of genetic ability using genomic data is the most effective, and the smaller the M_e, the higher the accuracy of EBV.

• Journal of Animal Science and Technology
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• 제48권1호
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• pp.15-20
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• 2006

국내에서 사용한 젖소 정액을 네 가지(한국형 보증종모우 정액, 농협 수입 보증종모우 정액, 미국산 수입 정액, 카나다산 수입 정액)로 분류하여 표현형 능력 및 유전능력을 비교하였다. 유전능력의 경우 농촌진흥청 축산연구소에 수행하고 있는 국가단위 젖소유전능력평가 결과를 이용하였다. 유량, 유지량 및 유단백량의 표현형 능력의 경우 미국산 수입 정액이 가장 우수하였고, 한국형 보증종모우 정액은 미국산 수입 정액과 유의한 차이를 보였다. 1991년 이후 태어난 보증종모우의 경우 유지량은 네 종류의 정액 사이에 유의한 차이가 없었다. 유량, 유지량, 유단백량, 유단백율 유전능력의 경우 네 종류 사이에 유의한 차이가 없었으며, 유지율의 경우 한국형 보증종모우 정액이 가장 우수하였다. 선형심사 최종점수 및 유방종합지수의 경우 카나다산 수입정액이 가장 우수하였으며, 한국형 보증종모우 정액과 유의한 차이를 보였다. MFP 및 KTPI의 경우 네 종류 사이에 유의한 차이가 없었다. 1991년 이후에 태어난 보증종모우의 유량 및 유단백량의 경우 네 종류 사이에 유의한 차이가 없었으나, 유지량, 유지율 및 유단백율의 경우 한국형 보증종모우 정액이 가장 우수하였고, 나머지 정액과 유의한 차이를 보였다. 선형심사 최종점수의 경우 한국형 보증종모우 정액, 미국산 수입정액 및 카나다산 수입정액 사이에 통계적으로 유의한 차이가 없었다. 유방종합지수의 경우 카나다산 수입정액이 가장 우수하였고, 한국형 보증종모우 정액과 유의한 차이가 났다. MFP의 경우 한국형 보증종모우 정액이 가장 우수하였고, 나머지 정액과 유의한 차이를 보였다. KTPI의 경우 한국형 보증종모우 정액, 미국산 수입정액 및 카나다산 수입정액 사이에 통계적으로 유의한 차이가 없었다.

• 한국산림과학회지
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• 제38권1호
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• pp.33-45
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• 1978

본(本) 연구(硏究)는 소나무천연집단(天然集團)의 유전변이(遺傳變異)를 분석(分析)하는데 목적(目的)이 있다. 1974년도(年度)의 선발(選拔)에 이어서 1975년도(年度)에 3개(個)소나무천연집단(天然集團) 각각(各各)으로부터 20주(株)씩의 개체(個體)가 선발(選拔)되고 또 그들의 풍매종자(風媒種子)가 채취(採取)되었으며 그 집단(集團)들의 소재지역(所在地域)과 상태(狀態)는 표(表) 1, 2 및 그림 1에 기술(記述)되어 있다. 그 집단(集團)들의 몇몇 형태학적특징(形態學的特徵)들은 이미 보고(報告)된 논문(論文)(II)에 상술(詳述)되어 있으며 거기에서는 명주(溟洲) 및 울진집단(蔚珍集團)이 수원집단(水原集團)에 비(比)해 직관적(直觀的)으로 보아 우량(優良)한 것으로 판단 되었다. 본(本) 논문(論文)에서는 앞서 발표(發表)된 논문(論文)(III)의 방법(方法)에 따라서 구과(毬果), 종자(種子), 종자익(種子翼)의 형태학적(形態學的)인 특성(特性)과 아울러 묘목(苗木)의 성장(成長) 및 그 침엽(針葉)의 특성(特性)이 조사(調査)되었으며 얻어진 결과(結果)는 다음과 같이 요약(要約)된다. 1. 각집단(各集團)에서 가장 가까운 측후소(測候所)에서 측정(測定)된 30년(年) (1931~1960)간(間)의 기록(記錄)을 평균(平均)해서 얻어진 기상자료(氣象資料)는 그림 2, 3, 4에 보인다. 조사(調査)된 기후조건(氣候條件)은 대체로 지역간(地域間)에 유사(類似)하지만 수원지역(水原地域)의 여름철 강우량(降雨量)과 겨울철 기온(氣溫)이 타지역(他地域)과 크게 달랐다. 2. 구과(毬果)의 생중량(生重量), 길이, 직경(直徑), 형상비(形狀比)의 측정치(測定値)는 표(表) 7에 기재(記載)되어 있으며 구과직경(毬果直徑)을 제외(除外)한 다른 모든 조사(調査)된 특성(特性)은 집단간(集團間), 집단내가계간(集團內家系間)에 유의(有意)한 통계적차이(統計的差異)가 인정(認定)되었다. 3. 종자(種子)와 종자익(種子翼)의 형태학적특성(形態學的特性)은 표(表) 8, 9에 상술(詳述)되었으며 종자(種子)와 종자익(種子翼)의 길이 및 형상비(形狀比) 그리고 종자중량(種子重量)에서는 집단간(集團間), 집단내가계간(集團內家系間)에 유의차(有意差)가 인정(認定)되지만 다른 특성(特性)에서는 집단간(集團間)에 유의차(有意差)가 인정(認定)되지 않았다. 구과(毬果)와 종자(種子) 특성간(特性間)의 상관계수(相關係數)의 값은 표(表) 10에 주어져 있으며 비교(比較)된 특성(特性)의 대부분(大部分)에서 정(正)의 상관계수(相關係數)가 인정(認定)되었다. 4. 차대(次代)의 1-0묘(苗)와 1-1묘(苗)의 묘고성장(苗高成長)에서 집단간(集團間), 집단내가계간(集團內家系間) 통계적(統計的)인 유의차(有意差)가 인정(認定)되었지만 근원경(根元徑)에서는 집단내(集團內) 가계간(家系間)에만 그 차(差)가 인정(認定)되었다. 표(表)13에 보인바와 같이 묘목(苗木)의 성장(成長)과 종자(種子)의 특성간(特性間)에는 대부분 상관(相關)이 통계학적(統計學的)으로 인정(認定)되지 않았다. 5. 3개집단(個集團)의 각가계별(各家系別)로 묘목(苗木)에 있어서 침엽양면(針葉兩面)의 기공열수(氣孔列數)와 거치밀도(鋸齒密度)가 측정(測定)되었으며 표(表)14에 보이는 것처럼 거치밀도(鋸齒密度)에서는 집단간(集團間), 집단내가계간(集團內家系間)에 유의차(有意差)가 인정(認定)되었지만 기공별(氣孔別)에서는 집단간(集團間) 차이(差異)가 인정(認定)되지 않았다. 그 결과(結果)는 논문(論文)(III)의 것과 다르며 그 원인(原因)의 하나는 선발(選拔)된 집단(集團)의 다양성(多樣性) 때문인 것으로도 생각된다. 차대(次代)와 모수(母樹)와의 침엽형질(針葉形質)에서의 상관(相關)은 표(表)15에 보이는 바와 같이 대체로 인정(認定)되지 않았다.

• Genomics & Informatics
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• 제18권2호
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• pp.14.1-14.11
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• 2020

Phenotyping is a major issue for wheat agriculture to meet the challenges of adaptation of wheat varieties to climate change and chemical input reduction in crop. The need to improve the reuse of observations and experimental data has led to the creation of reference ontologies to standardize descriptions of phenotypes and to facilitate their comparison. The scientific literature is largely under-exploited, although extremely rich in phenotype descriptions associated with cultivars and genetic information. In this paper we propose the Wheat Trait Ontology (WTO) that is suitable for the extraction and management of scientific information from scientific papers, and its combination with data from genomic and experimental databases. We describe the principles of WTO construction and show examples of WTO use for the extraction and management of phenotype descriptions obtained from scientific documents.

• Genomics & Informatics
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• 제14권4호
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• pp.149-159
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• 2016

With the success of the genome-wide association studies (GWASs), many candidate loci for complex human diseases have been reported in the GWAS catalog. Recently, many disease prediction models based on penalized regression or statistical learning methods were proposed using candidate causal variants from significant single-nucleotide polymorphisms of GWASs. However, there have been only a few systematic studies comparing existing methods. In this study, we first constructed risk prediction models, such as stepwise linear regression (SLR), least absolute shrinkage and selection operator (LASSO), and Elastic-Net (EN), using a GWAS chip and GWAS catalog. We then compared the prediction accuracy by calculating the mean square error (MSE) value on data from the Korea Association Resource (KARE) with body mass index. Our results show that SLR provides a smaller MSE value than the other methods, while the numbers of selected variables in each model were similar.

• BMB Reports
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• 제47권6호
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• pp.348-353
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• 2014

The speed of sound (SOS) value is an indicator of bone mineral density (BMD). Previous genome-wide association (GWA) studies have identified a number of genes, whose variations may affect BMD levels. However, their biological implications have been elusive. We re-analyzed the GWA study dataset for the SOS values in skeletal sites of 4,659 Korean women, using a gene-set analysis software, GSA-SNP. We identified 10 common representative GO terms, and 17 candidate genes between these two traits (PGS < 0.05). Implication of these GO terms and genes in the bone mechanism is well supported by the literature survey. Interestingly, the significance levels of some member genes were inversely related, in several gene-sets that were shared between two skeletal sites. This implies that biological process, rather than SNP or gene, is the substantial unit of genetic association for SOS in bone. In conclusion, our findings may provide new insights into the biological mechanisms for BMD.

• International Journal of Industrial Entomology and Biomaterials
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• 제19권1호
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• pp.143-154
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• 2009

Single nucleotide polymorphisms (SNPs) are the most frequent form of variation in the genome of any organism. Owing to their greater abundance, they are considered useful for identifying cultivars, construction of higher density linkage maps, and detection of genes (QTLs) associated with complex agronomic traits and diseases. Although, SNPs have been used recently for constructing a high density genetic map in silkworm and a set of 118 SNPs have been identified in tasar silkworms, not much progress has been made in sericulture to utilize the vast potential of SNPs. Thus, this review mainly focuses on some of the important methods of SNP discovery, validation and genotyping. Emphasis has also been given to the possible uses of SNP genotyping in the improvement of silkworms and their host plants.

• Journal of Plant Biotechnology
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• 제47권2호
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• pp.107-117
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• 2020

Flower industry is now growing due to the development of economy in many countries. Simultaneously, needs from consumers in flower market are varied widely. To satisfy the needs from consumers and deal with a variety of diseases from a lots of pathogens as well as climate change, new elite flower cultivars should be released in flower market. For this purpose, conventional and biotechnological techniques can be employed to make good cultivar. Therefore, this review describes the general overview of flower breeding techniques including cross-hybridization, mutation breeding and genetic transformation systems. Also, breeding systems for ornamentals derived from plant tissue culture such as embryo culture, in vitro fertilization, ovary/ovule culture and haploid production were reviewed. Furthermore, in this study recent development of the generation of new flower cultivars using marker-assisted breeding, plant transformation including particle bombardment and Agrobacterium tumefaciens as well as genome-editing technology were described. This review will be contributed to the development and releasement of new flower cultivars with horticulturally useful traits in the future.

• 한국수산과학회지
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• 제34권4호
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• pp.419-421
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• 2001

Heritability estimations of masu salmon smelt at underyearing of age were described. Masu salmon was taken from aquaculture station of Mori in Japan. After fertilization, the offsprings in each family were reared in separate egg trays and fingerling tanks. The percentage of fish in each tank which smoltified at 11-month old was recorded, and environmental and genetic factors influencing the percentage smoltification were also studied. Percentage of smoltification was not significantly affected by the number of fish held in a tank, or fish density (correlation coefficient 0.10). However, there was a high correlation ($0.821\~0.565$) between smelt percentage and growth related traits of fish in a family. Heritability estimated from total data was $0.47\pm0.13$, when effects of tanks were ignored.