Genetic Parameters and Genome-Wide Association Studies for Body Size Traits of Shuxuan Cattle in China

In domestic cattle,the body size traits have important implications in terms of breed characteristics and production performance.Shuxuan cattle is a dual-purpose breed mainly raised in Sichuan province,China,for which we have known less about the genetic parameters and underlying candidate genes in relation to the body size traits.In this study,we obtained the genome-wide single nucleotide polymorphisms(SNPs)using the Illumina Bovine BeadChip in 275 Shuxuan cattle.These SNPs were first used for estimating genetic parameters for the withers height(WH)and diagonal body length(BL).Using the bivariate animal model,the estimates(±standard error)of heritabilities were 0.71±0.22 and 0.49±0.29 for BL,and their genetic correlation was 0.64±0.37.Second,the genome-wide association study(GWAS)was performed.However,these did not result into genome-wide significant SNPs for both WH and BL traits.According to a less stringent suggestive significance,some positional candidate genes were found,and some of them(such as FAM110B,TAS1R2,PAX3,and FHIT)were previously reported in literature to be associated with body size traits in cattle.In conclusion,we estimated the genetic parameters in Shuxuan cattle using genomic information for the first time,which are required for implementing the genomic selection programs in the future.

Genome-wide association study for starch content and constitution in sorghum(Sorghum bicolor(L.) Moench)

Starch is the most important component in endosperm of sorghum grain.Usually,two types of starch are present:amylose(AM)and amylopectin(AP).The levels of AM and AP contents play a significant role in the appearance,structure,and quality of sorghum grains and in marketing applications.In the present study,a panel of 634 sorghum(Sorghum bicolor(L.)Moench)accessions were evaluated for starch,AM,and AP contents of grain,which included a mini core collection of 242 accessions from the International Crops Research Institute for the Semi-Arid Tropics(ICRISAT)in India,and 252 landraces and 140 cultivars from China.The average starch content was 67.64%and the average AM and AP contents were 20.19 and 79.81%,respectively.We developed a total of 260000 high-confidence single nucleotide polymorphism(SNP)markers in the panel of 634 accessions of S.bicolor using specific locus amplified fragment sequencing(SLAF-seq).We performed genome-wide association studies(GWAS)of starch,AM,and AM/AP of grain and SNP markers based on a mixed linear model(MLM).In total,70 significant association signals were detected for starch,AM,and AM/AP ratio of grain with P<4.452×10^-7,of which 10 SNPs were identified with significant starch,51 SNPs were associated with AM,and nine SNPs were associated with the AM/AP ratio.The Gene Ontology(GO)analysis identified 12 candidate genes at five QTLs associated with starch metabolism within the 200-kb intervals,located on chromosomes 1,5,6,and 9.Of these genes,Sobic.006G036500.1 encodes peptidyl-prolyl cis-trans-isomerase CYP38 responsible for hexose monophosphate shunt(HMS)and Sobic.009G071800 encodes 6-phospho-fructokinase(PFK),which is involved in the embden-meyerhof pathway(EMP).Kompetitive allele specific PCR(KASP)markers were developed to validate the GWAS results.The C allele is correlated with a high starch content,while the T allele is linked with a low level of starch content,and provides reliable haplotypes for MAS in sorghum quality improvement.

Genome-Wide Association Study for Certain Carcass Traits and Organ Weights in a Large White×Minzhu Intercross Porcine Population

Porcine carcass traits and organ weights have important economic roles in the swine industry. A total of 576 animals from a Large White×Minzhu intercross population were genotyped using the Illumina PorcineSNP60K Beadchip and were phenotyped for 10 traits, speciifcally, backfat thickness （6-7 libs）, carcass length, carcass weight, foot weight, head weight, heart weight, leaf fat weight, liver weight, lung weight and slaughter body weight. The genome-wide association study （GWAS） was assessed by Genome Wide Rapid Association using the mixed model and regression-genomic control approach. A total of 31 single nucleotide polymorphisms （SNPs） （with the most signiifcant SNP being MARC0033464, P value=6.80×10-13） were located in a 9.76-Mb （31.24-41.00 Mb） region on SSC7 and were found to be signiifcantly associated with one or more carcass traits and organ weights. High percentage of phenotypic variance explanation was observed for each trait ranging from 31.21 to 67.42%. Linkage analysis revealed one haplotype block of 495 kb, in which the most signiifcant SNP being MARC0033464 was contained, on SSC7 at complete linkage disequilibrium. Annotation of the pig reference genome suggested 6 genes （GRM4, HMGA1, NUDT3, RPS10, SPDEF and PACSIN1） in this candidate linkage disequilibrium （LD） interval. Functional analysis indicated that the HMGA1 gene presents the prime biological candidate for carcass traits and organ weights in pig, with potential application in breeding programs.

Myopia genetics in genome-wide association and postgenome-wide association study era

Genome-wide association studies(GWAS) of myopia and refractive error have generated exciting results and identified novel risk-associated loci. However, the interpretation of the findings of GWAS of complex diseases is not straightforward and has remained challenging. This review provides a brief summary of the main focus on the advantages and limitations of GWAS of myopia, with potential strategies that may contribute to further insight into the genetics of myopia in the post-GWAS or omics era.

Identification of New Resistance Loci Against Sheath Blight Disease in Rice Through Genome-Wide Association Study

Sheath blight(SB) caused by the soil borne pathogen Rhizoctonia solani is one of the most serious global rice diseases. Breeding resistant cultivar is the most economical and effective strategy to control the disease. However, no rice varieties are completely resistant to SB, and only a few reliable quantitative trait loci(QTLs) linked with SB resistance have been identified to date. In this study, we conducted a genome-wide association study(GWAS) of SB resistance using 299 varieties from the rice diversity panel 1(RDP1) that were genotyped using 44 000 high-density single nucleotide polymorphism(SNP) markers. Through artificial inoculation, we found that only 36.5% of the tested varieties displayed resistance or moderate resistance to SB. In particular, the aromatic and aus sub-populations displayed higher SB resistance than the tropical japonica(TRJ), indica and temperate japonica sub-populations. Seven varieties showed similar resistance levels to the resistant control YSBR1. GWAS identified at least 11 SNP loci significantly associated with SB resistance in the three independent trials, leading to the identification of two reliable QTLs, qSB-3 and qSB-6, on chromosomes 3 and 6. Using favorable alleles or haplotypes of significantly associated SNP loci, we estimated that both QTLs had obvious effects on reducing SB disease severity and can be used for enhancing SB resistance, especially in improving SB resistance of TRJ sub-population rice varieties. These results provided important information and genetic materials for developing SB resistant varieties through breeding.

Re-evaluation of ABO gene polymorphisms detected in a genomewide association study and risk of pancreatic ductal adenocarcinoma in a Chinese population

Pancreatic cancer is a fatal malignancy with an increasing incidence in Shanghai, China. A genomewide association study(GWAS) and other work have shown that ABO alleles are associated with pancreatic cancer risk. We conducted a population-based case-control study involving 256 patients with pathologically confirmed pancreatic ductal adenocarcinoma(PDAC) and 548 healthy controls in Shanghai, China, to assess the relationships between GWAS-identified ABO alleles and risk of PDAC. Carriers of the C allele of rs505922 had an increased cancer risk [adjusted odds ratio(OR) = 1.42, 95% confidence interval(CI): 1.02-1.98] compared to TT carriers. The T alleles of rs495828 and rs657152 were also significantly associated with an elevated cancer risk(adjusted OR = 1.58, 95% CI: 1.17-2.14; adjusted OR = 1.51, 95% CI: 1.09-2.10). The rs630014 variant was not associated with risk. We did not find any significant gene-environment interaction with cancer risk using a multifactor dimensionality reduction(MDR) method. Haplotype analysis also showed that the haplotype CTTC was associated with an increased risk of PDAC(adjusted OR = 1.46, 95% CI: 1.12-1.91) compared with haplotype TGGT. GWAS-identified ABO variants are thus also associated with risk of PDAC in the Chinese population.

Comparison of dimension reduction-based logistic regression models for case-control genome-wide association study:principal components analysis vs.partial least squares

With recent advances in biotechnology, genome-wide association study （GWAS） has been widely used to identify genetic variants that underlie human complex diseases and traits. In case-control GWAS, typical statistical strategy is traditional logistical regression （LR） based on single-locus analysis. However, such a single-locus analysis leads to the well-known multiplicity problem, with a risk of inflating type I error and reducing power. Dimension reduction-based techniques, such as principal component-based logistic regression （PC-LR）, partial least squares-based logistic regression （PLS-LR）, have recently gained much attention in the analysis of high dimensional genomic data. However, the perfor- mance of these methods is still not clear, especially in GWAS. We conducted simulations and real data application to compare the type I error and power of PC-LR, PLS-LR and LR applicable to GWAS within a defined single nucleotide polymorphism （SNP） set region. We found that PC-LR and PLS can reasonably control type I error under null hypothesis. On contrast, LR, which is corrected by Bonferroni method, was more conserved in all simulation settings. In particular, we found that PC-LR and PLS-LR had comparable power and they both outperformed LR, especially when the causal SNP was in high linkage disequilibrium with genotyped ones and with a small effective size in simulation. Based on SNP set analysis, we applied all three methods to analyze non-small cell lung cancer GWAS data.

Pathway-based analysis of genome-wide association study of circadian phenotypes

Sleepiness affects normal social life, which attracts more and more attention. Circadian phenotypes contribute to obvious individual differences in susceptibility to sleepiness. We aimed to identify candidate single nucleotide polymorphisms（SNPs） which may cause circadian phenotypes, elucidate the potential mechanisms, and generate corresponding SNP-gene-pathways. A genome-wide association studies（GWAS） dataset of circadian phenotypes was utilized in the study. Then, the Identify Candidate Causal SNPs and Pathways analysis was employed to the GWAS dataset after quality control filters. Furthermore, genotype-phenotype association analysis was performed with HapMap database. Four SNPs in three different genes were determined to correlate with usual weekday bedtime,totally providing seven hypothetical mechanisms. Eleven SNPs in six genes were identified to correlate with usual weekday sleep duration, which provided six hypothetical pathways. Our results demonstrated that fifteen candidate SNPs in eight genes played vital roles in six hypothetical pathways implicated in usual weekday bedtime and six potential pathways involved in usual weekday sleep duration.

Genome-wide association study for rib eye muscle area in a Large White×Minzhu F_2 pig resource population

Rib eye muscle area（REMA） is an economically important trait and one of the main selection criteria for breeding in the swine industry. In the genome-wide association study（GWAS）, the Illumina Porcine SNP60 Bead Chip containing 62 163 single nucleotide polymorphisms（SNPs） was used to genotype 557 pigs from a porcine Large White×Minzhu intercross population. The REMA（at the 5th–6th, 10th–11th and the last ribs） was measured after slaughtered at the age of（240±7） d for each animal. Association tests between REMA trait and SNPs were performed via the Genome-Wide Rapid Association using the Mixed Model and Regression-Genomic Control（GRAMMAR-GC） approach. From the Ensembl porcine database, SNP annotation was implemented using Sus scrofa Build 10.2. Thirty-three SNPs on SSC12 and 3 SNPs on SSC2 showed significant association with REMA at the last rib at the chromosome-wide significance level. None of the SNPs of REMA at the 5th–6th rib and only a few numbers of the SNPs of REMA at the 10th–11th ribs were found in this study. The Haploview V3.31 program and the Haplo.Stats R package were used to detect and visualize haplotype blocks and to analyze the association of the detected haplotype blocks with REMA at the last rib. A linkage analysis revealed that 4 haplotype blocks contained 4, 4, 2, and 4 SNPs, respectively. Annotations from pig reference genome suggested 2 genes（NOS2, NLK） in block 1（266 kb）, one gene（TMIGD1） in block 2（348 kb）, and one gene（MAP2K4） in block 3（453 kb）. A functional analysis indicated that MYH3 and MYH13 genes are the potential genes controlling REMA at the last rib. We screened several candidate intervals and genes based on the SNPs location and the gene function, and inferred that NOS2 and NLK genes maybe the main genes of REMA at the last ribs.

A genome-wide association study identifies novel genetic loci that modify pharmacokinetic-pharmacodynamic responses to clopidogrel

OBJECTIVE Genetic variants in the pharmacokinetic(PK)mechanism are the main underlying factors that modify the antiplatelet efficacy of clopidogrel.Hence,joint analysis of genetic variants that modify pharmacodynamic(PD)and PK responses to clopidogrel should be effective for identifying the genetic variants affecting the antiplatelet response to the drug.METHODS A genome-wide association study was conducted to identify new genetic loci that modify PD responses to clopidogrel and its active metabolite H4 in 115 Chinese patients with coronary heart disease(CHD).RESULTS We identified novel variants in two transporter genes(rs12456693 in SLC14A2 and rs2487032 in ABCA1)and in N6AMT1(rs2254638)associated with clopidogrel-treated P2Y12reaction unit(PRU)and plasma H4 concentration.The associations between these single nucleotide polymorphisms(SNPs)and PK parameters of clopidogrel and H4 were observed in 31 additional CHD patients(P<0.05).The new variants,together with CYP2C19*2 and clinical factors,dramatically improved the predictability of PRU variability to 37.7%compared with the published value of approximately 20%.The function of these SNPs on the activation of clopidogrel was validated in 32 liver S9 fractions,and the N6AMT1 rs2254638 T variant was found to be associated with decreased formation of H4(P=0.0386).Meanwhile,N6AMT1 rs2254638 was further identified to exert a marginal risk effect for MACE in an independent CHD patient cohort(OR:1.428,95%CI:0.978-2.086,P=0.0653,FDR=0.4726).In conclusion,we systematically identified new genetic variants as risk factors for the reduced efficacy of clopidogrel.CONCLUSION Our study findings enhanced the understanding of the absorption and metabolic mechanisms that influence PD responses to clopidogrel treatment.

Genome-Wide Association Study in Thai Tsunami Survivors Identified Risk Alleles for Posttraumatic Stress Disorder

Posttraumatic stress disorder (PTSD) is a psychiatric disorder found in individuals afflicted by a traumatic event. Multiple environmental and genetic factors can contribute to PTSD susceptibility. Since it is rare to find members of the same family afflicted by the same catastrophic event, it is not practical to determine PTSD susceptibility genes by a gene linkage analysis. A natural disaster, such as the 2004 Tsunami, provided us with a rare chance for a genetic analysis of PTSD. To identify SNPs associated with PTSD susceptibility, we conducted a genome-association study (GWAS) in Thai-Tsunami survivors. Initial phase of the study with 396 chronic PTSD patients and 457 controls, we identified top ninety SNPs (P -4), which were further assessed in the second phase with 395 chronic PTSD patients and 798 controls. Two SNPs (rs267950 and rs954406), were identified in the second phase, and subjected to fine mapping using a data set from both phases. SNP rs267943 showed the strongest association with PTSD susceptibility and was in complete linkage disequilibrium with SNP rs267950 with P = 6.15 × 10-8, OR = 1.46 and 95% CI = 1.19 - 1.79, reaching genome-wide significance. SNP rs267943 is located on chromosome 5 in the intron of the death-associated protein 1 (DAP1) gene and, when linked to a synthetic promoter, could regulate transcription. To our knowledge, this is the first GWAS for PTSD susceptibility in an Asian population which could provide an important insight into the genetic contribution of PTSD and may lead to new treatment strategies for PTSD.

Statistical analysis for genome-wide association study

In the past few years, genome-wide association study （GWAS） has made great successes in identifying genetic susceptibility loci underlying many complex diseases and traits. The findings provide important genetic insights into understanding pathogenesis of diseases. In this paper, we present an overview of widely used approaches and strategies for analysis of GWAS, offered a general consideration to deal with GWAS data. The issues regarding data quality control, population structure, association analysis, multiple comparison and visual presentation of GWAS results are discussed; other advanced topics including the issue of missing heritability, meta-analysis, setbased association analysis, copy number variation analysis and GWAS cohort analysis are also briefly introduced.

Epidemiological studies of esophageal cancer in the era of genome-wide association studies

Esophageal cancer(EC) caused about 395000 deaths in 2010. China has the most cases of EC and EC is the fourth leading cause of cancer death in China. Esophageal squamous cell carcinoma(ESCC) is the predominant histologic type(90%-95%), while the incidence of esophageal adenocarcinoma(EAC) remains extremely low in China. Traditional epidemiological studies have revealed that environmental carcinogens are risk factors for EC. Molecular epidemiological studies revealed that susceptibility to EC is influenced by both environmental and genetic risk factors. Of all the risk factors for EC, some are associated with the risk of ESCC and others with the risk of EAC. However, the details and mechanisms of risk factors involved in the process for EC are unclear. The advanced methods and techniques used in human genome studies bring a great opportunity for researchers to explore and identify the details of those risk factors or susceptibility genes involved inthe process of EC. Human genome epidemiology is a new branch of epidemiology, which leads the epidemiology study from the molecular epidemiology era to the era of genome wide association studies(GWAS). Here we review the epidemiological studies of EC(especially ESCC) in the era of GWAS, and provide an overview of the general risk factors and those genomic variants(genes, SNPs, miRNAs, proteins) involved in the process of ESCC.

Host genetic factors affecting hepatitis B infection outcomes:Insights from genome-wide association studies

The clinical outcome of hepatitis B virus(HBV) infection depends on the success or failure of the immune responses to HBV,and varies widely among individuals,ranging from asymptomatic self-limited infection,inactive carrier state,chronic hepatitis,cirrhosis,hepatocellular carcinoma,to liver failure,depending on the success or failure of immune response to HBV.Genome-wide association studies(GWAS) identified key genetic factors influencing the pathogenesis of HBV-related traits.In this review,we discuss GWAS for persistence of HBV infection,antibody response to hepatitis B vaccine,and HBV-related advanced liver diseases.HBV persistence is associated with multiple genes with diverse roles in immune mechanisms.The strongest associations are found within the classical human leukocyte antigen(HLA) genes,highlighting the central role of antigen presentation in the immune response to HBV.Associated variants affect both epitope binding specificities and expression levels of HLA molecules.Several other susceptibility genes regulate the magnitude of adaptive immune responses,determining immunity vs tolerance.HBV persistence and nonresponse to vaccine share the same risk variants,implying overlapping genetic bases.On the other hand,the risk variants for HBV-related advanced liver diseases are largely different,suggesting different host-virus dynamics in acute vs chronic HBV infections.The findings of these GWAS are likely to pave the way for developing more effective preventive and therapeutic interventions by personalizing the management of HBV infection.

Genetic polymorphisms and gastric cancer risk: a comprehensive review synopsis from meta-analysis and genome-wide association studies

Objective: In the past few decades, more than 500 reports have been published on the relationship between single nucleotide polymorphisms(SNPs) on candidate genes and gastric cancer(GC) risk. Previous findings have been disputed and are controversial. Therefore, we performed this article to summarize and assess the credibility and strength of genetic polymorphisms on the risk of GC.Methods: We used Web of Science, PubMed, and Medline to identify meta-analyses published before July 30 th, 2018 that assessed associations between variants on candidate genes and the risk of GC. Cumulative epidemiological evidence of statistical associations was assessed combining Venice criteria and a false-positive report probability(FPRP) test.Results: Sixty-one variants demonstrated a significant association with GC risk, whereas 29 demonstrated no association. Nine variants on nine genes were rated as presenting strong cumulative epidemiological evidence for a nominally significant association with GC risk, including APE1(rs1760944), DNMT1(rs16999593), ERCC5(rs751402), GSTT1(null/presence), MDM2(rs2278744), PPARG(rs1801282), TLR4(rs4986790), IL-17 F(rs763780), and CASP8(rs3834129). Eleven SNPs were rated as moderate, and 33 SNPs were rated as weak. We also used the FPRP test to identify 13 noteworthy SNPs in five genome-wide association studies.Conclusions: Sixty-one variants are significantly associated with GC risk, and 29 variants are not associated with GC risk;however, five variants on five genes presented strong evidence for an association upgraded from moderate. Further study of these variants may be needed in the future. Our study also provides referenced information for the genetic predisposition to GC.

Implications of discoveries from genome-wide association studies in current cardiovascular practice

Genome-wide association studies(GWAS)have identified several genetic variants associated with coronary heart disease(CHD),and variations in plasma lipoproteins and blood pressure(BP).Loci corresponding to CDKN2A/CDKN2B/ANRIL,MTHFD1L,CELSR2,PSRC1 and SORT1 genes have been associated with CHD,and TMEM57,DOCK7,CELSR2,APOB,ABCG5,HMGCR,TRIB1,FADS2/S3,LDLR,NCAN and TOMM40-APOE with total cholesterol.Similarly,CELSR2-PSRC1-SORT1,PCSK9,APOB,HMGCR,NCAN-CILP2-PBX4,LDLR,TOMM40-APOE,and APOC1-APOE are associated with variations in low-density lipoprotein cholesterol levels.Altogether,forty,forty three and twenty loci have been associated with high-density lipoprotein cholesterol,triglycerides and BP phenotypes,respectively.Some of these identified loci are common for all the traits,some do not map to functional genes,and some are located in genes that encode for proteins not previously known to be involved in the biological pathway of the trait.GWAS have been successful at identifying new and unexpected genetic loci common to diseases and traits,thus rapidly providing key novel insights into disease biology.Since genotype information is fixed,with minimum biological variability,it is useful in early life risk prediction.However,these variants explain only a small proportion of the observed variance of these traits.Therefore,the utility of genetic determinants in assessing risk at later stages of life has limited immediate clinical impact.The future application of genetic screening will be in identifying risk groups early in life to direct targeted preventive measures.

Validation of the Red Pericarp Gene from 419 Rice Landraces in Guangxi via Genome-wide Association Studies

Rice has different colors of pericarp, such as red, white and black. Red rice pericarp is rich in proanthocyanins, which have antioxidant properties and are beneficial to human health. In the present study, we analyzed the red-pericarp gene Rc of 419 rice landraces in Guangxi by genome-wide association study （GWAS）, and validated that the Rc gene regulated the red periearp trait in flee. By analyzing the genomie DNA of 97 red-pericarp flee eultivars, we identified two new alleles in C139 and C323. Then, the exons of Rcc＇9 and Rcc were sequenced with Sanger method, and the results demonstrated that the natural mutations within Re ene resulted in the two alleles Rcc and Rcc.

Genome-wide association of 10 horticultural traits with expressed sequence tag-derived SNP markers in a collection of lettuce lines

Genetic diversity, population structure, and genome-wide marker-trait association analyses were conducted on a special collection of 298 homozygous lettuce(Lactuca sativa L.) lines. Each of these lines was derived from a single plant that had been genotyped with 384 SNP markers using LSGermOPA. They included 122 butterhead, 53 romaine, 63 crisphead, 53 leaf and 7 stem types. Genetic diversity among these plants was assessed by pairwise comparison based on 322 high-quality SNP markers selected from 384 SNPs. Only 258 unique genotypes were identified among the 298 lines because 26 pairs or small groups(a total of 66 lines) shared identical genotypes. The average genetic similarity coefficient(GS) among these unique genotypes was 63.9% with a range of 40.6% to 99.8%. A phylogenetic tree was constructed based on the genotypic data. The most likely number of populations was estimated to be two or six. Association analysis between the 322 SNP markers and 10 phenotypic traits using the 258 homozygous lines was performed by three different methods: single factor analysis, general linear model analysis, and mixed linear model analysis. Nine significant marker-trait associations(SMTAs) were detected at P < 0.0001 with all three methods and also when considering kinship and/or population structure for this collection, with five SMTAs for seed coat color, one for leaf undulation, two for leaf anthocyanin, and one for stem anthocyanin. These markers will be useful in marker-assisted selection after further validation with segregating populations.

Genome-Wide Association Analysis and Allelic Mining of Grain Shape-Related Traits in Rice

Excavating single nucleotide polymorphisms (SNPs) significantly associated with rice grain shape and predicting candidate genes through genome-wide association study (GWAS) can provide a theoretical basis for discovery and utilization of excellent genetic resources in rice. Based on 16 352 SNPs, 161 natural indica rice varieties with various grain sizes in southern China were used for GWAS of grain shape-related traits, referring to grain length (GL), grain width (GW), 1000-grain weight (TGW), and grain length/width (GLW). Phenotypic statistics showed that coefficient of variation values for these four traits GL, GW, TGW and GLW were 9.92%, 9.09%, 20.20% and 16.38%, respectively. Each trait showed a normal distribution, and there was a certain correlation between these traits. Through general linear model correlation analysis, a total of 38 significant loci were identified, and a range of 100 kb upstream and downstream of the significant loci was identified as the candidate interval. On chromosome 3, GS3 and qGL3 were found to regulate GL. On chromosome 6, TGW6 and GW6a were found to regulate TGW. Also, some QTLs related to grain shape were found on chromosomes 5 and 9. Besides that, using sequenced 3K-germplasm resources, we found that there are 22 overlapped varieties between these two natural populations. Twenty-six SNPs and fourteen haplotypes were identified in five regions of GS3 genes. The detection of multiple candidate genes/QTLs within the candidate interval is beneficial for further excavation of superior rice genetic resources.

Genome-Wide Association Studies Reveal New Genetic Targets for Five Panicle Traits of International Rice Varieties

Narrow genetic background is a key limiting factor in breeding stable high-yielding rice. The introduction and utilization of international rice core germplasm is an important way to increase the genetic diversity of domestic rice varieties. We conducted a genome-wide association study on 5 panicle traits of 315 rice accessions introduced from the international rice micro-core germplasm bank. Based on the tests from Yangzhou of China and Arkansas of American, environment exhibited a significant impacts on panicle length and primary branch number, while grain length, grain width and grain length/width ratio were insensitive to environment changes. We discovered a total of 7, 5, 10, 8 and 6 chromosomal regions or single nucleotide polymorphism marker loci that were significantly associated with primary branch number, panicle length, grain length, grain width and grain length/width ratio, respectively. Among them, eleven regions were associated with grain shape and one region associated with primary branch number, showing the good consistence in two different environments. Significant linear correlation was discovered between the average trait value and the number of favorable alleles carried by the varieties in all associated loci. Among the associated loci, varieties in aromatic and tropical japonica sub-groups possessed most favorable alleles, while those in temperate japonica sub-group contained the least. The domestic varieties mainly harbored unfavorable alleles in six of the associated loci being detected. On the contrary, 15 varieties from 11 different countries harbored more favorable alleles （as many as 30 or more） than the others. Remarkably, all these 15 varieties belonged to the tropical japonica sub-group. In conclusion, our study demonstrates that varieties in the tropical japonica sub-group had high potentials for breeding stable high-yielding rice. Based on this discovery, we proposed a new approach for improving the panicle traits of domestic rice by using tropical japonica varieties.