Yield response to water deficit in an upland rice mapping population: associations among traits and genetic markers

A population of recombinant inbred rice lines from a cross between the upland japonica cultivar Azucena and the upland indica cultivar Bala was evaluated in a series of upland field experiments. Water stress was imposed during the reproductive stage by managed irrigation during the dry season, while control treatments were maintained in aerobic, well-irrigated conditions. Water deficit resulted in a yield reduction of 17 to 50%. The genetic correlation between stress and control yields was quite high when stress was mild, and the heritability of yield was similar in stress and control treatments across both years of this study. Genetic correlations between secondary traits such as leaf rolling and drying and yield under stress varied from high (leaf drying) to insignificant (leaf rolling). Lines with superior yield tended to have fewer panicles and larger grain size than the high-yielding parent, Bala, even though the panicle number was positively correlated with yield and the thousand-grain weight was not associated with yield for the population as a whole. Analysis of quantitative trait loci (QTLs) for yield and yield components allowed the identification of 31 regions associated with growth or yield components. Superior alleles came from either parent. Several of the regions identified had also been reported for root mass at depth or maximum root length in this population in other studies made under controlled environments, and for leaf drying (LD) in field studies. However, the direction of the effect of QTLs was not consistent, which indicates that there was not necessarily a causal relationship between these secondary traits and performance. We conclude that mapping populations can provide novel insights on the actual relationships between yield components and secondary traits in stress and control environments and can allow identification of significant QTLs for yield components under drought stress.Abbreviations DAS Days after sowing - GPP Grains per panicle - QTL Quantitative trait locus - RWC Relative water content - SPP Spikelets per panicle - TGW Thousand-grain weight - VPD Vapor pressure deficit     

Genome-wide association mapping of yield and yield components of spring wheat under contrasting moisture regimes

Key message

A stable QTL that may be used in marker-assisted selection in wheat breeding programs was detected for yield, yield components and drought tolerance-related traits in spring wheat association mapping panel.

Abstract

Genome-wide association mapping has become a widespread method of quantitative trait locus (QTL) identification for many crop plants including wheat (Triticum aestivum L.). Its benefit over traditional bi-parental mapping approaches depends on the extent of linkage disequilibrium in the mapping population. The objectives of this study were to determine linkage disequilibrium decay rate and population structure in a spring wheat association mapping panel (n = 285–294) and to identify markers associated with yield and yield components, morphological, phenological, and drought tolerance-related traits. The study was conducted under fully irrigated and rain-fed conditions at Greeley, CO, USA and Melkassa, Ethiopia in 2010 and 2011 (five total environments). Genotypic data were generated using diversity array technology markers. Linkage disequilibrium decay rate extended over a longer genetic distance for the D genome (6.8 cM) than for the A and B genomes (1.7 and 2.0 cM, respectively). Seven subpopulations were identified with population structure analysis. A stable QTL was detected for grain yield on chromosome 2DS both under irrigated and rain-fed conditions. A multi-trait region significant for yield and yield components was found on chromosome 5B. Grain yield QTL on chromosome 1BS co-localized with harvest index QTL. Vegetation indices shared QTL with harvest index on chromosome 1AL and 5A. After validation in relevant genetic backgrounds and environments, QTL detected in this study for yield, yield components and drought tolerance-related traits may be used in marker-assisted selection in wheat breeding programs.     

Use of unlinked genetic markers to detect population stratification in association studies.

We examine the issue of population stratification in association-mapping studies. In case-control studies of association, population subdivision or recent admixture of populations can lead to spurious associations between a phenotype and unlinked candidate loci. Using a model of sampling from a structured population, we show that if population stratification exists, it can be detected by use of unlinked marker loci. We show that the case-control-study design, using unrelated control individuals, is a valid approach for association mapping, provided that marker loci unlinked to the candidate locus are included in the study, to test for stratification. We suggest guidelines as to the number of unlinked marker loci to use.     

A study of association between genetic markers in candidate genes and reproductive traits in one generation of a commercial broiler breeder hen population

Markers of alleles for three physiological candidate genes for reproductive traits, growth hormone (GHR), gonadotropin-releasing hormone receptor (GNRHR) and neuropeptide Y (NPY) were assessed for the association with the total egg production, number of double-yolked eggs and age at first egg in a single generation of a broiler breeder (Gallus gallus) pedigree dam line. Single-nucleotide polymorphisms and deletions were detected in the GHR, GNRHR and NPY genes. Genotypes were identified using a PCR-RFLP assay. The frequency of restriction enzyme+/-alleles in the population was for GHR 0.68 (NspI-) and 0.32 (NspI+), for NPY 0.78 (DraI+) and 0.22 (DraI-) and for GNRHR 0.54 (Bpu1102I+) and 0.46 (Bpu1102I-). Trait data from a total of 772 hens in 67 sire families from one generation of the pedigree dam line were recorded. However, the analysis used only the offspring of heterozygous sires to reduce the influence of selection and genetic background (n=33 sire families for GHR; n=14 sire families for NPY; n=36 sire families for GNRHR). A dominance effect of NPY on age at first egg and an additive effect of GNRHR on the number of double-yolked eggs were found (P<0.05).     

On coding genotypes for genetic markers with multiple alleles in genetic association study of quantitative traits

Background

In genetic association study of quantitative traits using F_∞ models, how to code the marker genotypes and interpret the model parameters appropriately is important for constructing hypothesis tests and making statistical inferences. Currently, the coding of marker genotypes in building F_∞ models has mainly focused on the biallelic case. A thorough work on the coding of marker genotypes and interpretation of model parameters for F_∞ models is needed especially for genetic markers with multiple alleles.

Results

In this study, we will formulate F_∞ genetic models under various regression model frameworks and introduce three genotype coding schemes for genetic markers with multiple alleles. Starting from an allele-based modeling strategy, we first describe a regression framework to model the expected genotypic values at given markers. Then, as extension from the biallelic case, we introduce three coding schemes for constructing fully parameterized one-locus F_∞ models and discuss the relationships between the model parameters and the expected genotypic values. Next, under a simplified modeling framework for the expected genotypic values, we consider several reduced one-locus F_∞ models from the three coding schemes on the estimability and interpretation of their model parameters. Finally, we explore some extensions of the one-locus F_∞ models to two loci. Several fully parameterized as well as reduced two-locus F_∞ models are addressed.

Conclusions

The genotype coding schemes provide different ways to construct F_∞ models for association testing of multi-allele genetic markers with quantitative traits. Which coding scheme should be applied depends on how convenient it can provide the statistical inferences on the parameters of our research interests. Based on these F_∞ models, the standard regression model fitting tools can be used to estimate and test for various genetic effects through statistical contrasts with the adjustment for environmental factors.     

Grain yield and correlated traits of bread wheat lines: Implications for yield improvement

Global wheat yields are suffering due to differences in regional climatic conditions and soil fertility. Plant breeders are continuously working to improve the yield per unit area of wheat crop through selecting superior lines as parents. The screening and field evaluation of available lines allow the selection of superior ones and subsequently improved varieties. Therefore, heritable distinctions among 33 bread wheat lines for yield and related attributes were assessed under field conditions. The experiment included thirty lines and three check varieties. Data relating to different plant characteristics was collected at maturity. Significant differences were recorded for yield and related traits of tested wheat lines and check varieties. Wheat lines V₆, V₁₂ and V₂₀ proved better with reduced number of days to reach anthesis and other desirable traits compared to check varieties. Days to start heading had strong correlation with spike length and number of spikelets spike^-1. Flag leaf area had positive relationship with peduncle length and yield related traits. The 1000-garin weight and grain yield were also correlated with each other. It is concluded that V₆, V₁₀ and V₂₀ proved better for all studied traits than the rest of the lines. Therefore, these lines could be used in wheat breeding program as parents to improve yield.     

An epigenome-wide association analysis of cardiac autonomic responses among a population of welders

DNA methylation is one of the potential epigenetic mechanisms associated with various adverse cardiovascular effects; however, its association with cardiac autonomic dysfunction, in particular, is unknown. In the current study, we aimed to identify epigenetic variants associated with alterations in cardiac autonomic responses. Cardiac autonomic responses were measured with two novel markers: acceleration capacity (AC) and deceleration capacity (DC). We examined DNA methylation levels at more than 472,506 CpG probes through the Illumina Infinium HumanMethylation450 BeadChip assay. We conducted separate linear mixed models to examine associations of DNA methylation levels at each CpG with AC and DC. One CpG (cg26829071) located in the GPR133 gene was negatively associated with DC values after multiple testing corrections through false discovery rate. Our study suggests the potential functional importance of methylation in cardiac autonomic responses. Findings from the current study need to be replicated in future studies in a larger population.     

Genome-wide association study reveals the genetic determinism of growth traits in a Gushi-Anka F2 chicken population

Chicken growth traits are economically important, but the relevant genetic mechanisms have not yet been elucidated. Herein, we performed a genome-wide association study to identify the variants associated with growth traits. In total, 860 chickens from a Gushi-Anka F₂ resource population were phenotyped for 68 growth and carcass traits, and 768 samples were genotyped based on the genotyping-by-sequencing (GBS) method. Finally, 734 chickens and 321,314 SNPs remained after quality control and removal of the sex chromosomes, and these data were used to carry out a GWAS analysis. A total of 470 significant single-nucleotide polymorphisms (SNPs) for 43 of the 68 traits were detected and mapped on chromosomes (Chr) 1–6, -9, -10, -16, -18, -23, and -27. Of these, the significant SNPs in Chr1, -4, and -27 were found to be associated with more than 10 traits. Multiple traits shared significant SNPs, indicating that the same mutation in the region might have a large effect on multiple growth or carcass traits. Haplotype analysis revealed that SNPs within the candidate region of Chr1 presented a mosaic pattern. The significant SNPs and pathway enrichment analysis revealed that the MLNR, MED4, CAB39L, LDB2, and IGF2BP1 genes could be putative candidate genes for growth and carcass traits. The findings of this study improve our understanding of the genetic mechanisms regulating chicken growth and carcass traits and provide a theoretical basis for chicken breeding programs.Subject terms: Genome-wide association studies, Genetic linkage study, Development, DNA sequencing, Animal breeding     

Selection in a cycling population: differential response among skeletal traits

Abstract Population density cycles influence phenotypic evolution through both density‐dependent selection during periods of high density and through enhanced genetic drift during periods of low density. We investigated the response of different phenotypic traits to the same density cycles in a population of the yellow‐necked mouse, Apodemus flavicollis, from Bia?owieza National Park in Poland. We examined nonmetric skull traits, skull and mandible size, skull and mandible shape, and transferrin allele frequencies. We found that all of the traits changed significantly over the seven‐year study period. The greatest changes in nonmetric traits and mandible size occurred during periods of increasing density, and the magnitude of changes in skull and mandible shape was correlated with the magnitude of density changes. Frequencies of transferrin alleles changed the most when population density was in decline. Changes among the five phenotypic traits were generally uncorrelated with one another, except for skull and mandible shape. Nonmetric traits were selectively neutral when assessed with Q_ST/F_ST analysis, whereas mandible size, mandible shape, and skull shape showed evidence of fairly strong selection. Selection on skull size was weak or nonexistent. We discuss how different assumptions about the genetic components of variance affect Q_ST estimates when phenotypic variances are substituted for genetic ones. We also found that change in mandible size, mandible shape, skull size, and skull shape were greater than expected under a neutral model given reasonable assumptions about heritability and effective population size.     

Revealing the genetic diversity of teosinte introgressed maize population by morphometric traits and microsatellite markers

Journal of Plant Biochemistry and Biotechnology - The present study comprised of 100 lines derived from teosinte × maize (DI-103) hybridization, which were evaluated for...     

A high-density rice genetic linkage map with 2275 markers using a single F2 population.

A 2275-marker genetic map of rice (Oryza sativa L.) covering 1521.6 cM in the Kosambi function has been constructed using 186 F2 plants from a single cross between the japonica variety Nipponbare and the indica variety Kasalath. The map provides the most detailed and informative genetic map of any plant. Centromere locations on 12 linkage groups were determined by dosage analysis of secondary and telotrisomics using > 130 DNA markers located on respective chromosome arms. A limited influence on meiotic recombination inhibition by the centromere in the genetic map was discussed. The main sources of the markers in this map were expressed sequence tag (EST) clones from Nipponbare callus, root, and shoot libraries. We mapped 1455 loci using ESTs; 615 of these loci showed significant similarities to known genes, including single-copy genes, family genes, and isozyme genes. The high-resolution genetic map permitted us to characterize meiotic recombinations in the whole genome. Positive interference of meiotic recombination was detected both by the distribution of recombination number per each chromosome and by the distribution of double crossover interval lengths.     

The genetic dissection of complex traits in a founder population

We estimated broad heritabilities (H(2)) and narrow heritabilities (h(2)) and conducted genomewide screens, using a novel association-based mapping approach for 20 quantitative trait loci (QTLs) among the Hutterites, a founder population that practices a communal lifestyle. Heritability estimates ranged from.21 for diastolic blood pressure (DBP) to.99 for whole-blood serotonin levels. Using a multipoint method to detect association under a recessive model we found evidence of major QTLs for six traits: low-density lipoprotein (LDL), triglycerides, lipoprotein (a) (Lp[a]), systolic blood pressure (SBP), serum cortisol, and whole-blood serotonin. Second major QTLs for Lp(a) and for cortisol were identified using a single-point method to detect association under a general two-allele model. The heritabilities for these six traits ranged from.37 for triglycerides to.99 for serotonin, and three traits (LDL, SBP, and serotonin) had significant dominance variances (i.e., H(2) > h(2)). Surprisingly, there was little correlation between measures of heritability and the strength of association on a genomewide screen (P>.50), suggesting that heritability estimates per se do not identify phenotypes that are influenced by genes with major effects. The present study demonstrates the feasibility of genomewide association studies for QTL mapping. However, even in this young founder population that has extensive linkage disequilibrium, map densities <5 cM may be required to detect all major QTLs.     

镜鲤繁殖群体的遗传结构及微卫星标记与经济性状的相关性分析

选用35个多态性微卫星分子标记对天津换新良种场镜鲤一个繁殖群体的有效等位基因数(Ae)、观测杂合度(Ho)、期望杂合度(He)、多态信息含量(PIC) 等进行了检测, 以卡方检验估计群体Hardy-Weinberg平衡。结果表明：在35个基因座共检测到118个等位基因, 平均等位基因数为3.37个, 每个座位检测到的等位基因数2~7个不等, 平均有效等位基因数为2.16, 观测杂合度平均值0.431, 无偏期望杂合度的平均值为0.4736, 平均多态信息含量0.42, 说明这个群体属于中度多态, 遗传多样性水平不高。卡方检验的P值显示多于半数的位点都发生了偏离。并将35个基因座的不同基因型与个体的体重、体长值进行了连锁分析, 得到了4个与体重、体长连锁的基因型, 并将所得结果与鲤鱼体长性状QTL定位结果进行对比, 其中HLJ319标记与QTL定位结果基本一致。分析了几个严重偏离平衡的基因型, 并讨论出现这种现象的可能原因。     

Linkage and allelic association of chromosome 5 cytokine cluster genetic markers with atopy and asthma associated traits

Linkage and association of polymorphic markers in the chromosome 5q31-q33 cytokine cluster to atopy and asthma associated phenotypes have been reported by a number of groups. To investigate this region, 29 polymorphic markers were used to genotype a combined set of 233 families. These markers were ordered based upon the genetic data, supplemented by published genetic and physical maps. Significant two-point linkage was observed for asthma (most significant marker IRF1, P = 0.0002) and atopy (CD14SNP, P = 0.0001). Allelic association was observed between D5S463 and atopy (P = 0.002) and the skin prick test index (P = 0.04). The data support the possibility of three asthma/atopy loci in the 5q31-q33 region, each with a relatively small effect.     

Genome-wide association mapping identifies markers associated with cane yield components and sucrose traits in the Louisiana sugarcane core collection

Sugarcane is an economically important crop for both food and biofuel industries. Marker-assisted breeding in sugarcane is becoming a reality with the recent development and deployment of markers linked with disease resistance genes. Large linkage disequilibrium in sugarcane makes genome-wide association studies (GWAS) a better alternative to biparental mapping to identify markers associated with agronomic traits. GWAS was conducted on a Louisiana core collection to identify marker-trait associations (MTA) for 11 cane yield and sucrose traits using single nucleotide polymorphism (SNP) and insertion-deletion (Indel) markers. Significant (P < .05) MTAs were identified for all traits where the top ranked markers explained up to 15% of the total phenotypic variation. High correlations (0.732 to 0.999) were observed between sucrose traits and 56 markers were found consistent across multiple traits. These markers following validation in more diverse populations could be used in marker-assisted selection of clones in sugarcane breeding program in Louisiana and elsewhere.     

Molecular dissection of the genetic relationships of source,sink and transport tissue with yield traits in rice

Source, sink, and translocation capacity of assimilates play important roles during the formation of grain yield. The present study was conducted to characterize the genetic bases of traits representing source, sink and transport tissue, and their relationships with yield traits in rice, by analyzing QTLs for these traits and various ratios among them. The genetic materials were a recombinant inbred population derived from a cross between two indica cultivars Zhenshan 97 and Minghui 63, the parents of the most-widely grown hybrid rice in China. Using a linkage map that covers a total of 1,796 cM based on 221 molecular marker loci, a total of 81 QTLs were identified for the 15 traits studied (three leaf areas as the source, total spikelets per panicle as the sink, the number of large vascular bundles in the stem as transport tissue, three source to sink ratios, three transport tissue to source ratios, one transport tissue to sink ratio and three yield traits). The amount of variation explained by individual QTLs ranged from 1.12% to 24.14%. Five QTLs were identified to show interaction effects with the environment, which explained from 3.19% to 9.15% of the variation. The results showed that close linkage or pleiotropy is the genetic basis for the correlations of grain yield traits with source, sink, transport tissue and the various ratios among them. Of the 25 QTLs identified for source-sink-transport tissue trait, and 43 for various ratios, 8 and 22 QTLs, respectively, were mapped to the similar genomic blocks harboring QTLs for yield traits, especially for grain weight. Co-location of QTLs for yield traits with those for ratios among source, sink and transport tissue may provide a genetic explanation for the physiological expression of yield traits, and also suggest that improvement in ratios among source, sink and transport tissue may result in improvement in yield potential.     

Analysis on additive effects and additive-by-additive epistatic effects of QTLs for yield traits in a recombinant inbred line population of rice

A linkage map consisting of 158 DNA markers were constructed by using a recombinant inbred line (RIL) population derived from the indica-indica rice cross Zhenshan 97B 2 Milyang 46. Quantitative trait loci (QTLs) conditioning grain yield and five yield component traits were determined at the one-locus and two-locus levels, and genotype-by-environment (GE) interactions were analyzed. Thirty-one QTLs were detected to have significant additive effects for yield traits, of which 12 also exhibited significant epistatic effects. Sixteen significant additive-by-additive (AA) interactions were detected, of which nine occurred between QTLs with own additive effects (M_epQTLs), four occurred between QTLs showing epistatic effects only (epQTLs), and three occurred between M_epQTLs and epQTLs. Significant GE interactions were found for six QTLs with additive effects and one AA interaction. Generally, the contributions to the phenotypic variation were higher due to QTL main effects than to epistatic effects. The detection of additive effects and AA effects of a QTL interfered with each other, indicating that the detection of QTLs with main effects, as well as the magnitude and directions of the additive effects, might vary depending on their interactions with other loci.     

Assessment of genetic diversity of landraces of Dendrocalamus hamiltonii using AFLP markers and association with biochemical traits

Fermented bamboo shoots are popular traditional food items of various ethnic groups of the northeastern India, especially in Manipur State. Dendrocalamus hamiltonii is an economically important bamboo species used to produce fermented bamboo shoots. We studied genetic variability of this bamboo species in Chandel and Imphal-East (commercial production districts), using AFLP molecular markers. Each of the selected primers detected polymorphisms and 1614 (95.8%) were found to be polymorphic. Cluster analysis based on Dice similarity coefficients using UPGMA differentiated the populations into two major groups. Principal coordinate analysis based on the AFLP data clearly separated the populations according to their genetic diversity and antioxidant activity. Four primers were tested through multiple regression analysis to identify marker-trait association between AFLP data and biochemical attributes, i.e., antioxidant activity and total cyanide content. The 273 bp generated by EcoRI-AAG(Joe)/MseI-CTC showed high positive correlation with antioxidant activity (r = 0.729, P < 0.01). The 396 bp generated by EcoRI-AAC(Ned)/MseI-CTG were negatively correlated with cyanide content (r = -0.694, P < 0.01). Thus, we found association of DNA markers with antioxidant activities and total cyanide content. These results could be of use for the identification of superior genotypes with desirable traits.     

水稻ILP标记遗传图谱的构建

内含子长度多态性(ILP)是一种基于PCR的新型分子标记, 具有许多突出的优点。我们先前利用已公布的籼稻品种93-11和粳稻品种日本晴的基因组序列数据, 已开发了172个水稻ILP标记。为了检验这些ILP标记的可靠性及其在遗传作图中的可用性, 利用一个BC1F1(日本晴/93-11//日本晴)群体, 构建了一张含172个ILP标记座位和13个SSR标记座位的水稻遗传图谱, 总长度为1 905.7 cM。比较显示, 图谱上所有标记的顺序与其物理顺序完全一致, 证明了利用ILP标记进行遗传作图的可行性和有效性。文中还对标记偏分离现象进行了分析, 发现在第6号染色体短臂上存在一个严重偏分离的区域。