Identification of QTL for flag leaf length in common wheat and their pleiotropic effects

Leaf size is an important factor contributing to the photosynthetic capability of wheat plants. It also significantly affects various agronomic traits. In particular, the flag leaves contribute significantly to grain yield in wheat. A recombinant inbred line (RIL) population developed between varieties with significant differences in flag leaf traits was used to map quantitative trait loci (QTL) of flag leaf length (FLL) and to evaluate its pleiotropic effects on five yield-related traits, including spike length (SL), spikelet number per spike (SPN), kernel number per spike (KN), kernel length (KL), and thousand-kernel weight (TKW). Two additional RIL populations were used to validate the detected QTL and reveal the relationships in different genetic backgrounds. Using the diversity arrays technology (DArT) genetic linkage map, three major QTL for FLL were detected, with single QTL in different environments explaining 8.6–23.3% of the phenotypic variation. All the QTL were detected in at least four environments, and validated in two related populations based on the designed primers. These QTL and the newly developed primers are expected to be valuable for fine mapping and marker-assisted selection in wheat breeding programs.     

Genetic mapping and quantitative trait locus analysis of fiber quality traits using a three-parent composite population in upland cotton (Gossypium hirsutum L.)

Composite cross populations (CP) developed from three or more cultivars/lines are frequently used to improve agronomic and economic traits in crop cultivar development programs. Employing CP in linkage map construction and quantitative trait locus (QTL) mapping may increase the marker density of upland cotton (Gossypium hirsutum L.) genetic maps, exploit more adequate gene resources and facilitate marker-assisted selection (MAS). To construct a relatively high-density map and identify QTL associated with fiber quality traits in upland cotton, three elite upland cultivars/lines, Yumian 1, CRI 35 and 7,235, were used to obtain the segregating population, Yumian 1/CRI 35//Yumian 1/7,235. A genetic map containing 978 simple sequence repeat (SSR) loci and 69 linkage groups was constructed; the map spanned 4,184.4 cM, covering approximately 94.1% of the entire tetraploid cotton genome. A total of 63 QTL were detected, explaining 8.1–55.8% of the total phenotypic variance: 11 QTL for fiber elongation, 16 QTL for fiber length, 9 QTL for fiber micronaire reading, 10 QTL for fiber strength and 17 QTL for fiber length uniformity. The genetic map and QTL detected for fiber quality traits are promising for further breeding programs of upland cotton with improved fiber quality.     

Mapping QTL for grain yield and other agronomic traits in post-rainy sorghum [Sorghum bicolor (L.) Moench]

Sorghum, a cereal of economic importance ensures food and fodder security for millions of rural families in the semi-arid tropics. The objective of the present study was to identify and validate quantitative trait loci (QTL) for grain yield and other agronomic traits using replicated phenotypic data sets from three post-rainy dry sorghum crop seasons involving a mapping population with 245 F₉ recombinant inbred lines derived from a cross of M35-1 × B35. A genetic linkage map was constructed with 237 markers consisting of 174 genomic, 60 genic and 3 morphological markers. The QTL analysis for 11 traits following composite interval mapping identified 91 QTL with 5–12 QTL for each trait. QTL detected in the population individually explained phenotypic variation between 2.5 and 30.3 % for a given trait and six major genomic regions with QTL effect on multiple traits were identified. Stable QTL across seasons were identified. Of the 60 genic markers mapped, 21 were found at QTL peak or tightly linked with QTL. A gene-based marker XnhsbSFCILP67 (Sb03g028240) on SBI-03, encoding indole-3-acetic acid-amido synthetase GH3.5, was found to be involved in QTL for seven traits. The QTL-linked markers identified for 11 agronomic traits may assist in fine mapping, map-based gene isolation and also for improving post-rainy sorghum through marker-assisted breeding.     

水稻QTL分析的研究进展

水稻许多重要的性状是由多基因控制的数量性状,经典的数量遗传学只能把数量性状作为一个整体进行研究。近年来．高密度分子标记连锁图的构建和有效的生物统计学方法的发展使人们对数量性状遗传基础的研究出现了革命性的变化。通过对不同群体内的个体或品系的分子标记基因型和表型数据的共分离分析,能对QTL进行检测和定位。本文对QTL定位的原理和方法进行了介绍,从QTL的数目和效应、上位性效应、QTL基因型与环境的互作、相关性状的QTL以及个体发育不同阶段的QTL等方面对水稻QTL分析的研究进展进行了综述。水稻基因组测序计划已经完成,本文还对基因组时代水稻QTL精细定位和克隆的方法进行了探讨,对QTL分析在水稻育种中的应用前景进行了展望。     

Exploring the genetic characteristics of 93-11 and Nipponbare recombination inbred lines based on the GoldenGate SNP assay

Understanding genetic characteristics in rice populations will facilitate exploring evolutionary mechanisms and gene cloning. Numerous molecular markers have been utilized in linkage map construction and quantitative trait locus (QTL) mappings. However, segregation-distorted markers were rarely considered, which prevented understanding genetic characteristics in many populations. In this study, we designed a 384-marker GoldenGate SNP array to genotype 283 recombination inbred lines (RILs) derived from 93-11 and Nipponbare Oryza sativa crosses. Using 294 markers that were highly polymorphic between parents, a linkage map with a total genetic distance of 1,583.2 cM was constructed, including 231 segregation-distorted markers. This linkage map was consistent with maps generated by other methods in previous studies. In total, 85 significant quantitative trait loci (QTLs) with phenotypic variation explained (PVE) values≥5% were identified. Among them, 34 QTLs were overlapped with reported genes/QTLs relevant to corresponding traits, and 17 QTLs were overlapped with reported sterility-related genes/QTLs. Our study provides evidence that segregation-distorted markers can be used in linkage map construction and QTL mapping. Moreover, genetic information resulting from this study will help us to understand recombination events and segregation distortion. Furthermore, this study will facilitate gene cloning and understanding mechanism of inter-subspecies hybrid sterility and correlations with important agronomic traits in rice.     

Association mapping of seed oil content in Brassica napus and comparison with quantitative trait loci identified from linkage mapping

Association mapping has been used increasingly in natural populations with rich genetic diversity to detect DNA-based markers that are associated with important agronomic traits. Brassica napus is an important oil crop with limited genetic diversity. "New-type" B. napus that is introgressed with subgenomic components from related species has been developed to broaden the genetic basis of "traditional" B. napus. In this study, new-type B. napus lines and a collection of traditional B. napus varieties from different countries were used as two different populations to evaluate seed oil content and to determine the efficacy of association mapping by comparison with previous study of linkage mapping. Relatively rich genetic diversity, but a higher level of linkage disequilibrium was observed in the new-type B. napus as compared with the traditional B. napus. Similarly, a larger variation in oil content and a greater number of associated markers were detected in the population of new-type B. napus. Meanwhile, more than half of the genetic loci, to which the associated markers corresponded, were located within the quantitative trait loci intervals identified previously in linkage mapping experiments, which demonstrated the power of association mapping in B. napus.     

The genetic architecture of Drosophila sensory bristle number

We have mapped quantitative trait loci (QTL) for Drosophila mechanosensory bristle number in six recombinant isogenic line (RIL) mapping populations, each of which was derived from an isogenic chromosome extracted from a line selected for high or low, sternopleural or abdominal bristle number and an isogenic wild-type chromosome. All RILs were evaluated as male and female F(1) progeny of crosses to both the selected and the wild-type parental chromosomes at three developmental temperatures (18 degrees, 25 degrees, and 28 degrees ). QTL for bristle number were mapped separately for each chromosome, trait, and environment by linkage to roo transposable element marker loci, using composite interval mapping. A total of 53 QTL were detected, of which 33 affected sternopleural bristle number, 31 affected abdominal bristle number, and 11 affected both traits. The effects of most QTL were conditional on sex (27%), temperature (14%), or both sex and temperature (30%). Epistatic interactions between QTL were also common. While many QTL mapped to the same location as candidate bristle development loci, several QTL regions did not encompass obvious candidate genes. These features are germane to evolutionary models for the maintenance of genetic variation for quantitative traits, but complicate efforts to understand the molecular genetic basis of variation for complex traits.     

QTL mapping and the genetic basis of adaptation: recent developments

Quantitative trait loci (QTL) mapping has been used in a number of evolutionary studies to study the genetic basis of adaptation by mapping individual QTL that explain the differences between differentiated populations and also estimating their effects and interaction in the mapping population. This analysis can provide clues about the evolutionary history of populations and causes of the population differentiation. QTL mapping analysis methods and associated computer programs provide us tools for such an inference on the genetic basis and architecture of quantitative trait variation in a mapping population. Current methods have the capability to separate and localize multiple QTL and estimate their effects and interaction on a quantitative trait. More recent methods have been targeted to provide a comprehensive inference on the overall genetic architecture of multiple traits in a number of environments. This development is important for evolutionary studies on the genetic basis of multiple trait variation, genotype by environment interaction, host–parasite interaction, and also microarray gene expression QTL analysis.     

Mapping quantitative trait loci in multiple populations of Arabidopsis thaliana identifies natural allelic variation for trichome density

The majority of biological traits are genetically complex. Mapping the quantitative trait loci (QTL) that determine these phenotypes is a powerful means for estimating many parameters of the genetic architecture for a trait and potentially identifying the genes responsible for natural variation. Typically, such experiments are conducted in a single mapping population and, therefore, have only the potential to reveal genomic regions that are polymorphic between the progenitors of the population. What remains unclear is how well the QTL identified in any one mapping experiment characterize the genetics that underlie natural variation in traits. Here we provide QTL mapping data for trichome density from four recombinant inbred mapping populations of Arabidopsis thaliana. By aligning the linkage maps for these four populations onto a common physical map, the results from each experiment were directly compared. Seven of the nine QTL identified are population specific while two were mapped in all four populations. Our results show that many lineage-specific alleles that either increase or decrease trichome density persist in natural populations and that most of this genetic variation is additive. More generally, these findings suggest that the use of multiple populations holds great promise for better understanding the genetic architecture of natural variation.     

Genome-wide association mapping of Fusarium head blight resistance in contemporary barley breeding germplasm

Utilization of quantitative trait loci (QTL) identified in bi-parental mapping populations has had limited success for improving complex quantitative traits with low to moderate heritability. Association mapping in contemporary breeding germplasm may lead to more effective marker strategies for crop improvement. To test this approach, we conducted association mapping of two complex traits with moderate heritability; Fusarium head blight (FHB) severity and the grain concentration of mycotoxin associated with disease, deoxynivalenol (DON). To map FHB resistance in barley, 768 breeding lines were evaluated in 2006 and 2007 in four locations. All lines were genotyped with 1,536 SNP markers and QTL were mapped using a mixed model that accounts for relatedness among lines. Average linkage disequilibrium within the breeding germplasm extended beyond 4 cM. Four QTL were identified for FHB severity and eight QTL were identified for the DON concentration in two independent sets of breeding lines. The QTL effects were small, explaining 1–3% of the phenotypic variation, as might be expected for complex polygenic traits. We show that using breeding germplasm to map QTL can complement bi-parental mapping studies by providing independent validation, mapping QTL with more precision, resolving questions of linkage and pleiotropy, and identifying genetic markers that can be applied immediately in crop improvement.     

A consensus linkage map of common carp (Cyprinus carpio L.) to compare the distribution and variation of QTLs associated with growth traits

The ability to detect and identify quantitative trait loci (QTLs) in a single population is often limited. Analyzing multiple populations in QTL analysis improves the power of detecting QTLs and provides a better understanding of their functional allelic variation and distribution. In this study, a consensus map of the common carp was constructed, based on four populations, to compare the distribution and variation of QTLs. The consensus map spans 2371.6 cM across the 42 linkage groups and comprises 257 microsatellites and 421 SNPs, with a mean marker interval of 3.7 cM/marker. Sixty-seven QTLs affecting four growth traits from the four populations were mapped to the consensus map. Only one QTL was common to three populations, and nine QTLs were detected in two populations. However, no QTL was common to all four populations. The results of the QTL comparison suggest that the QTLs are responsible for the phenotypic variability observed for these traits in a broad array of common carp germplasms. The study also reveals the different genetic performances between major and minor genes in different populations.     

作物数量性状基因座定位及分析研究进展

近年来,分子数量遗传学的快速发展,使作物复杂数量性状尤其是经济性状的QTL研究取得了巨大进展,大大促进了复杂数量性状的遗传改良和分子操纵。本文从分子标记连锁图谱的构建、QTL定位力方法及效应分析、精细定位和QTL验证及应用等方面综述了二十多年来作物QTL的研究进展,讨论当前QTL研究中存在的问题,并展望了作物QTL研究的发展前景。     

Efficiency of selective genotyping for genetic analysis of complex traits and potential applications in crop improvement

Selective genotyping of individuals from the two tails of the phenotypic distribution of a population provides a cost efficient alternative to analysis of the entire population for genetic mapping. Past applications of this approach have been confounded by the small size of entire and tail populations, and insufficient marker density, which result in a high probability of false positives in the detection of quantitative trait loci (QTL). We studied the effect of these factors on the power of QTL detection by simulation of mapping experiments using population sizes of up to 3,000 individuals and tail population sizes of various proportions, and marker densities up to one marker per centiMorgan using complex genetic models including QTL linkage and epistasis. The results indicate that QTL mapping based on selective genotyping is more powerful than simple interval mapping but less powerful than inclusive composite interval mapping. Selective genotyping can be used, along with pooled DNA analysis, to replace genotyping the entire population, for mapping QTL with relatively small effects, as well as linked and interacting QTL. Using diverse germplasm including all available genetics and breeding materials, it is theoretically possible to develop an “all-in-one plate” approach where one 384-well plate could be designed to map almost all agronomic traits of importance in a crop species. Selective genotyping can also be used for genomewide association mapping where it can be integrated with selective phenotyping approaches. We also propose a breeding-to-genetics approach, which starts with identification of extreme phenotypes from segregating populations generated from multiple parental lines and is followed by rapid discovery of individual genes and combinations of gene effects together with simultaneous manipulation in breeding programs.     

Mapping quantitative trait loci in inbred backcross lines of Lycopersicon pimpinellifolium (LA1589).

Although tomato has been the subject of extensive quantitative trait loci (QTLs) mapping experiments, most of this work has been conducted on transient populations (e.g., F2 or backcross) and few homozygous, permanent mapping populations are available. To help remedy this situation, we have developed a set of inbred backcross lines (IBLs) from the interspecific cross between Lycopersicon esculentum cv. E6203 and L. pimpinellifolium (LA1589). A total of 170 BC2F1 plants were selfed for five generations to create a set of homozygous BC2F6 lines by single-seed descent. These lines were then genotyped for 127 marker loci covering the entire tomato genome. These IBLs were evaluated for 22 quantitative traits. In all, 71 significant QTLs were identified, 15% (11/71) of which mapped to the same chromosomal positions as QTLs identified in earlier studies using the same cross. For 48% (34/71) of the detected QTLs, the wild allele was associated with improved agronomic performance. A number of new QTLs were identified including several of significant agronomic importance for tomato production: fruit shape, firmness, fruit color, scar size, seed and flower number, leaf curliness, plant growth, fertility, and flowering time. To improve the utility of the IBL population, a subset of 100 lines giving the most uniform genome coverage and map resolution was selected using a randomized greedy algorithm as implemented in the software package MapPop (http://www.bio.unc.edu/faculty/vision/lab/ mappop/). The map, phenotypic data, and seeds for the IBL population are publicly available (http://soldb.cit.cornell.edu) and will provide tomato geneticists and breeders with a genetic resource for mapping, gene discovery, and breeding.     

远交群体动态性状基因定位的似然分析Ⅰ.理论方法

受动物遗传育种中用来估计动态性状育种值的随机回归测定日模型思想的启发 ,将关于时间 (测定日期 )的Legendre多项式镶嵌在遗传模型的每个遗传效应中 ,以刻画QTL对动态性状变化过程的作用 ,从而建立起动态性状基因定位的数学模型。利用远交设计群体 ,阐述了动态性状基因定位的似然分析原理 ,推导了定位参数似然估计的EM法两步求解过程。结合动态性状遗传分析的特点和普通数量性状基因定位研究进展 ,还提出了有关动态性状基因定位进一步研究的设想     

Germplasm-regression-combined (GRC) marker-trait association identification in plant breeding: a challenge for plant biotechnological breeding under soil water deficit conditions

In the past 20 years, the major effort in plant breeding has changed from quantitative to molecular genetics with emphasis on quantitative trait loci (QTL) identification and marker assisted selection (MAS). However, results have been modest. This has been due to several factors including absence of tight linkage QTL, non-availability of mapping populations, and substantial time needed to develop such populations. To overcome these limitations, and as an alternative to planned populations, molecular marker–trait associations have been identified by the combination between germplasm and the regression technique. In the present preview, the authors (1) survey the successful applications of germplasm–regression–combined (GRC) molecular marker–trait association identification in plants; (2) describe how to do the GRC analysis and its differences from mapping QTL based on a linkage map reconstructed from the planned populations; (3) consider the factors that affect the GRC association identification, including selections of optimal germplasm and molecular markers and testing of identification efficiency of markers associated with traits; and (4) finally discuss the future prospects of GRC marker–trait association analysis used in plant MAS/QTL breeding programs, especially in long-juvenile woody plants when no other genetic information such as linkage maps and QTL are available.     

Multiple-interval mapping for quantitative trait loci controlling endosperm traits

Endosperm traits are trisomic inheritant and are of great economic importance because they are usually directly related to grain quality. Mapping for quantitative trait loci (QTL) underlying endosperm traits can provide an efficient way to genetically improve grain quality. As the traditional QTL mapping methods (diploid methods) are usually designed for traits under diploid control, they are not the ideal approaches to map endosperm traits because they ignore the triploid nature of endosperm. In this article, a statistical method considering the triploid nature of endosperm (triploid method) is developed on the basis of multiple-interval mapping (MIM) to map for the underlying QTL. The proposed triploid MIM method is derived to broadly use the marker information either from only the maternal plants or from both the maternal plants and their embryos in the backcross and F2 populations for mapping endosperm traits. Due to the use of multiple intervals simultaneously to take multiple QTL into account, the triploid MIM method can provide better detection power and estimation precision, and as shown in this article it is capable of analyzing and searching for epistatic QTL directly as compared to the traditional diploid methods and current triploid methods using only one (or two) interval(s). Several important issues in endosperm trait mapping, such as the relation and differences between the diploid and triploid methods, variance components of genetic variation, and the problems if effects are present and ignored, are also addressed. Simulations are performed to further explore these issues, to investigate the relative efficiency of different experimental designs, and to evaluate the performance of the proposed and current methods in mapping endosperm traits. The MIM-based triploid method can provide a powerful tool to estimate the genetic architecture of endosperm traits and to assist the marker-assisted selection for the improvement of grain quality in crop science. The triploid MIM FORTRAN program for mapping endosperm traits is available on the worldwide web (http://www.stat.sinica.edu.tw/chkao/).     

亚麻主要农艺与品质相关性状的QTL定位

为了全面了解亚麻产量和品质相关性状的遗传基础,为亚麻基因克隆和分子标记辅助育种提供理论依据,在已构建SNP连锁遗传图谱的基础上,以LH-89为父本,R43为母本构建F2:3家系QTL定位群体,用R/QTL软件采用复合区间作图法对13个农艺和品质性状进行QTL定位。结果表明:(1)该研究共检测出35个QTL位点,与粗脂肪及其组成成分相关的QTL有20个,与农艺性状相关的QTL有15个;其中:亚油酸和粗脂肪各5个,亚麻酸、千粒重各4个,棕榈酸、株高、工艺长度各3个,硬脂酸、分枝数各2个,单株果数、果粒数、单株粒重、油酸各1个。(2)共有18个QTL的表型贡献率超10%(主效基因),其中农艺性状定位8个主效基因,品质性状定位10个主效基因。     

Linkage analysis of quantitative traits in an interspecific cross of tomato (lycopersicon esculentum x lycopersicon pimpinellifolium) by means of genetic markers

Linkage relationships between loci affecting quantitative traits (QTL) and marker loci were examined in an interspecific cross between Lycopersicon esculentum and Lycopersicon pimpinellifolium. Parental lines differed for six morphological markers and for four electrophoretic markers. Almost 1700 F-2 plants were scored with respect to the genetic markers and also with respect to 18 quantitative traits. Major genes affecting the quantitative traits were not found, but out of 180 possible marker x trait combinations, 85 showed significant quantitative effects associated with the genetic markers. The average marker-associated main effect was on the order of 6% of the mean value of the trait. Most of the main effects were apparently due to linkage of QTL to the marker loci rather than to pleiotropy. Fourteen of the traits showed at least one highly significant effect of opposite sign to the overall difference between the parental lines, demonstrating the ability of this design to uncover cryptic genetic variation. Significant variance and skewness effects on the quantitative traits were found to be associated with the genetic markers, suggesting the possible presence of loci affecting the variance and shape of quantitative trait distribution in a population. Most marker-associated quantitative effects showed some degree of dominance, generally in the direction of the L. pimpinellifolium parent. When the significant marker-associated effects were examined in pairs, 12% showed significant interaction effects. The results of this study illustrate the potential usefulness of this type of analysis for the detailed genetic investigation of quantitative trait variation in suitably marked populations.     

Fine mapping quantitative trait loci affecting milk production traits on bovine chromosome 6 in a Chinese Holstein population

To fine map the previously detected quantitative trait loci （QTLs） affecting milk production traits on bovine chromosome 6 （BTA6）, 15 microsatellite markers situated within an interval of 14.3 cM spanning from BMS690 to BM4528 were selected and 918 daughters of 8 sires were genotyped. Two mapping approaches, haplotype sharing based LD mapping and single marker regression mapping, were used to analyze the data. Both approaches revealed a quantitative trait locus （QTL） with significant effects on milk yield, fat yield and protein yield located in the segment flanked by markers BMS483 and MNB209, which spans a genetic distance of 0.6 cM and a physical distance of 1.5 Mb. In addition, the single marker regression mapping also revealed a QTL affecting fat percentage and protein percentage at marker DIK2291. Our fine mapping work will facilitate the cloning of candidate genes underlying the QTLs for milk production traits.