QTL analysis for some quantitative traits in bread wheat

Quantitative trait loci (QTL) analysis was conducted in bread wheat for 14 important traits utilizing data from four different mapping populations involving different approaches of QTL analysis. Analysis for grain protein content (GPC) sug- gested that the major part of genetic variation for this trait is due to environmental interactions. In contrast, pre-harvest sprouting tolerance (PHST) was controlled mainly by main effect QTL (M-QTL) with very little genetic variation due to environmental interactions; a major QTL for PHST was detected on chromosome arm 3AL. For grain weight, one QTL each was detected on chromosome arms 1AS, 2BS and 7AS. QTL for 4 growth related traits taken together detected by different methods ranged from 37 to 40; nine QTL that were detected by single-locus as well as two-locus analyses were all M-QTL. Similarly, single-locus and two-locus QTL analyses for seven yield and yield contributing traits in two populations respectively allowed detection of 25 and 50 QTL by composite interval mapping (CIM), 16 and 25 QTL by multiple-trait composite interval mapping (MCIM) and 38 and 37 QTL by two-locus analyses. These studies should prove useful in QTL cloning and wheat improvement through marker aided selection.

QTL analysis of leaf photosynthetic rate and related physiological traits in rice(Oryza sativa L.)

Photosynthesis is one of the most important factors that influence the biomass and yield. Recently, more attention has been paid to genetic study on rice photosynthesis and rice breeding for the physiological traits related to high efficient photosynthesis. Chlorophyll content, stomatal resistance, and transpiration rate were very important physiological traits related to photosynthesis. But until now, no genetic study on these traits has been reported. A DH population derived from anther culture of ZYQ8/JX17, a typical indica/japonica hybrid was developed,

Genetic Analysis of Cotton Fiber Traits by Molecular Markers

1.Development of EST-SSRs derived from G.barbadense:One hundred and nineteen EST-SSRs were developed based on 98 unique ESTs from a cDNA library constructed in our laboratory using developing fibers from G.barbadense cv.3-79.Among the SSRs,trinucleotide AAG appeared

Genetic Analysis of Main Plant Type-related Traits in Bitter Gourd(Momordica charantia L.)

In this study,the cultivated bitter gourd inbred line‘Foli 112’and the wild bitter gourd accession THMC170 were used as female(P1)and male(P2)parent,respectively,to obtain 4 generations(P1,P2,F1 and F2)through self-crossing and hybridization.The mixed major gene plus polygene inheritance model of plant quantitative trait was used to perform genetic analysis for 5 plant type-related traits including the number of internode,leaf length,leaf width,stem width and internode length in bitter gourd.Results showed that the inheritance of internode number,leaf length and leaf width was in accordance with E-6 model which involved two pairs of equi-dominant major genes with additive-dominant polygene model;the stem width was controlled by additive-dominance-epistasis polygene inheritance model(C-0 model);the inheritance of internode length involved 2 pairs of equi-additive major genes with additive-dominant polygene model(E-4 model).Meanwhile,the heritability(h2)of stem width and internode number was 20.08%and 39.28%,respectively,indicating that they were vulnerable to environment impacts;leaf length,leaf width and internode length had a higher heritability of 51.50%,52.16%and 64.36%,respectively;the inheritance of leaf length was mainly controlled by major gene(the heritability of major gene was 40.75%),indicating that early-generation selection was better for leaf length,while the inheritance of leaf width and internode length was mainly controlled by mutiple minor genes,indicating that it was better to select these two parameters for late generation.

QTLs analysis of rice peduncle vascular bundle and panicle traits

The vascular bundle in plants plays an important role intransportation of photosynthetic products, mineral nutri-ents, water, arid so on. Significant positive correlationswere found between grain yield, panicle traits and the No.of peduncle vascular bundles. So, it is very important tostudy the inheritance of peduncle vascular bundle, whichis a quantitative trait.

Analysis of genetic effects and correlations for nutrient quality traits of indica rice in different environments

Understanding the variation for the expressionof genes in different environments is one of themajor goals in qualitative genetics. In this pa-per, the genetic models for quantitative traitsof endosperm in cereal crops were used to eval-uate the seed, cytoplasm and maternal geneticeffects as well as the genotype × environment(GE) interaction effects, and to predict thebreeding value of parents and genotypic corre-lation for nutrient quality traits of indica rice (Oryza sativa L.).

Genetic analysis of morphological index and its related taxonomic traits for classification of indica

The Cheng index distinguishes indica andjaponica rice based on six taxonomic traits.This index has been widely used for classifi- cation of indica and japonica varieties in China.In this study,a double haploid(DH)popula-tion derived from anther culture of ZYQ8/JX17 F,a typical inter-subspecies hybrid,was used to investigate the six taxonomictraits,i.e.leaf hairiness(LH),color of hullwhen heading(CHH),hairiness of hull(HH),length of the first and second panicle internode(LPI),length/width of grain(L/W),andphenol reaction(PH).The morphological in- dex(MI)was also calculated.Based on themolecular linkage map constructed from this

Genetic analysis of quality traits in intersubspecies crosses of rice

Indica and japonica rices are two subspecies ofAsia cultivated rice.Their grain qualities exista significant difference.The objective of thispaper is to study the genetic control of qualitytraits in intersubspecies crosses of rice.In 1991,4 japonica varieties with widecompatibility,PC311,Zhenxiqiuguang,Lun-hui 422,and Ce 03 were crossed with 5 indicavarieties,3037,Zaoxiandang 18,IR36,Minghui 63,and Yangdao 4 according to NC(?)design.The 20 hybrids using japonica as ma-

Analysis of genetic relationships between grain milling quality traits and plant agronomic traits of rice

Since seed and maternal plant are in different generations,the grain milling traits and plant agronomic traits of rice are based on differentgenetic models.Using the genetic modelswhich could estimate covariance componentsbetween two traits with unequal design matri-ces,we analyzed the gentic relationships be-

Interspecific Chromosome Substitution Lines as Genetic Resources for Improvement,Trait Analysis and Genomic Inference

The genetic base that cotton breeders commonly use to improve Upland cultivars is very narrow.The AD-genome species Gossypium barbadense,G.tomentosum,and G.mustelinum are part of

Quantitative trait loci detection of E dwardsiella tarda resistance in Japanese flounder Paralichthys olivaceus using bulked segregant analysis

In recent years, Edwardsiella tarda has become one of the most deadly pathogens of Japanese fl ounder( Paralichthys olivaceus), causing serious annual losses in commercial production. In contrast to the rapid advances in the aquaculture of P. o livaceus, the study of E. tarda resistance-related markers has lagged behind, hindering the development of a disease-resistant strain. Thus, a marker-trait association analysis was initiated, combining bulked segregant analysis(BSA) and quantitative trait loci(QTL) mapping. Based on 180 microsatellite loci across all chromosomes, 106 individuals from the F1333(♀: F0768 ×♂: F0915)(Nomenclature rule: F+year+family number) were used to detect simple sequence repeats(SSRs) and QTLs associated with E. tarda resistance. After a genomic scan, three markers(Scaffold 404-21589, Scaffold 404-21594 and Scaffold 270-13812) from the same linkage group(LG)-1 exhibited a signifi cant difference between DNA, pooled/bulked from the resistant and susceptible groups( P <0.001). Therefore, 106 individuals were genotyped using all the SSR markers in LG1 by single marker analysis. Two different analytical models were then employed to detect SSR markers with different levels of signifi cance in LG1, where 17 and 18 SSR markers were identifi ed, respectively. Each model found three resistance-related QTLs by composite interval mapping(CIM). These six QTLs, designated q E1–6, explained 16.0%–89.5% of the phenotypic variance. Two of the QTLs, q E-2 and q E-4, were located at the 66.7 c M region, which was considered a major candidate region for E. tarda resistance. This study will provide valuable data for further investigations of E. tarda resistance genes and facilitate the selective breeding of disease-resistant Japanese fl ounder in the future.

An Assessment Scale for Evaluating the Experimental Design Ability of Elementary Science Teachers Based on Primary Trait Analysis

In this study,an assessment scale for evaluating the experimental design ability of elementary science teachers was constructed based on primary trait analysis.This assessment scale contains three first-level indexes and eleven second-level indexes.The corresponding weights of indexes were determined by the objective weighting method.The scores of all the descriptions of the indexes were also assigned.After a trial test,this assessment scale was verified to be reliable and valid for evaluating the experimental design ability of elementary science teachers.

Hitchhiking Effect Mapping: A New Approach for Discovering Agronomic Important Genes

Besides the natural selection, the crops cultivated today have experienced two episodes of strong artificial selection, domestic and modern breeding. Domestication led to giant genetic structure differentiation between cultivars and their wild species, while modern breeding made further genetic structure differentiation between the modern varieties and the landraces. In a population, diversity of the loci under strong selection is significantly lower than that of other loci. At the same time, diversity in the genomic regions flanking these selected loci also declines in the process of selection. This phenomenon is called hitchhiking effects or selection sweep in genetics. Genomic regions with selection sweep （haplotype block） could be detected after draft genome scanning （genome typing） with molecular markers in a number of released varieties or natural populations. Marker/trait association analysis in these regions would detect the loci （or QTLs） even the favored alleles （genes） in breeding or natural adaptation. Fine scanning of these genomic regions would help to determine the sizes of haplotype blocks and to discover the key genes, thereby providing very valuable information for isolation of the key genes and molecular design of new varieties. Establishment of high density genetic linkage maps in the major crops and availability of high throughput genotyping platform make it possible to discover agronomic important genes through marker/trait association analysis. On the basis of available publications, we give a brief introduction of the hitchhiking effect mapping approach in this paper using plant height, 1 000-grain weight, and phosphorus-deficiency tolerance as examples in wheat.

Cytological Correlation Between Flower and Vegetative Shoot Development from Immature Embryo-Derived Calli in Wheat

In this paper, the traits of immature embryo culture from 45 genotypes of bread wheat were investigated in detail, and trait correlation analysis in combination with histomorphological examination was used to study the cytological origin of flower as well as the correlation between it and vegetative shoot development from the calli. The rate of floral development in the subculture was highly significantly and positively related to that of the differentiation culture, which reveals that the genetic system of floral development from immature embryo-derived calli in wheat was highly correspondent and stable. The rate of floral development was related neither to the traits in the dedifferentiation culture, nor to the vegetative shoot formation from the total induced calli, but significantly and positively related to that of the calli without leaf-like green spots in the differentiation culture. These findings indicate the partial correlation as well as differentiation between flower and vegetative shoot development. The floral development might only be associated with the genetic system controlling organ regeneration, while vegetative shoots formed from the two ways, including somatic embryogenesis and organ regeneration.

Parental Selection in Rice Cultivar Improvement

The evaluation of rice （Oryza safiva L.） cultivars assists breeders in identifying useful trait relationships and in selecting parents as donors of specific traits. This study was conducted to compare long-grain rice cultivars using genotype x trait （GT） biplot analysis and determine potential donors of traits related to grain yield and quality. Seventeen cultivars in the 2005 and 2006 Uniform Regional Rice Nursery in Beaumont, Texas, USA were analyzed for 20 traits using GT biplot analysis. The GT biplots showed the diversity among cultivars with regards to yield-related traits. Cultivars recommended as donor parents were： Trenasse, Spring, Presidio, and Cocodrie for high grain yield and head rice rate Trenasse and Presidio for semi-dwarfness; Banks for tall plant height; Wells for high flag leaf area, panicle weight, and number and mass of filled grains per panicle; Hidalgo for high tiller density; Francis for high number of spikelets per panicle; Spring and Trenasse for short flowering duration; Cheniere for more days to heading and maturity and Spring for less days; and Spring and Hidalgo for high grain weiqht. Breeders can use these cultivars with specific traits to increase qrain yield and quality.

Identification of quantitative trait loci and epistasis for root characteristics and root exudations in maize (Zea mays L.) under deficient phosphorus

The phosphorus uptake （PU） in above-ground parts of plant, root characteristics and root exudations as well as the quantitative trait loci （QTLs） associated with these characteristics were determined for a F2：3 population derived from the cross of two contrasting maize （Zea mays L.） genotypes, 082 and Yel07. A total of 241 F2：3 families were evaluated in replicated trials under deficient phosphorus conditions in 2007 at two sites （Kaixian County and Southwest University, Chongqing, P. R. China）. The results show pleiotropy and close linkage among QTLs. Four common regions in different environments were in bnlg100- bnlg1268b （bins 1.02） for QTL of H＋, bnlg1268a-umc1290a （bins 1.09） for QTL of AP （acid phospbatase activity）, dupssrl5- P 1MT/a （bins 6.06） for QTLs of PU （phosphorus uptake） and RW （root weight）, and P IM3/d-P1M3/g （bins9.04） for QTLs of PU and AP. These QTLs are non-environment or minor QTLs x environment. By epistatic analysis, three main QTLs and eighteen QTLs x QTLs interactions were detected for the seven measured characteristics. These QTLs may affect trait expression by epistatic interaction with the other loci, and make a substantial contribution to phosphorus utilization efficiency, which should be considered when breeding maize varieties with high P efficiency. Two regions were detected in dupssrl 5- P1MT/a （bins 6.06） for QTL of RW and P1M3/d- P 1M3/g （bins 9.04） for QTL of PU and AP. They were detected in two different environments and by two methods of QTL analysis, which were useful for marker-assisted selection.

Methods for Population-Based eQTL Analysis in Human Genetics

Gene expression is a critical process in biological system that is influenced and modulated by many factors including genetic variation. Expression Quantitative Trait Loci（e QTL） analysis provides a powerful way to understand how genetic variants affect gene expression. For genome wide e QTL analysis, the number of genetic variants and that of genes are large and thus the search space is tremendous. Therefore, e QTL analysis brings about computational and statistical challenges. In this paper, we provide a comprehensive review of recent advances in methods for e QTL analysis in population-based studies. We first present traditional pairwise association methods, which are widely used in human genetics. To account for expression heterogeneity, we investigate the methods for correcting confounding factors. Next, we discuss newly developed statistical learning methods including Lasso-based models. In the conclusion, we provide an overview of future method development in analyzing e QTL associations. Although we focus on human genetics in this review, the methods are applicable to many other organisms.