植物数量性状基因定位研究概述

植物重要的性状多为数量性状。长期以来,人类一直寻求解释植物数量性状的遗传规律以便对其进行遗传操纵。现代分子生物技术的发展为植物数量性状基因的定位、分离等研究提供了条件。本文从数量性状基因座(QTL)作图群体类型及其特点,QTL定位方法,植物QTL研究现状,以及QTL精细定位、克隆、利用等方面进行了综述,并对今后植物QTL研究进行了展望。     

植物数量性状基因定位研究概述

植物重要的性状多为数量性状。长期以来,人类一直寻求解释植物数量性状的遗传规律以便对其进行遗传操纵。现代分子生物技术的发展为植物数量性状基因的定位、分离等研究提供了条件。本文从数量性状基因座(QTL)作图群体类型及其特点,QTL定位方法,植物QTL研究现状,以及QTL精细定位、克隆、利用等方面进行了综述,并对今后植物QTL研究进行了展望。     

民勤绿洲—荒漠过渡带植物叶性状的研究

以民勤绿洲—荒漠过渡带20种主要植物为研究对象,通过对叶片6个功能性状的测定,分析荒漠植物叶性状的变异及相关性,比较不同功能群植物叶性状的差异性,探讨荒漠植物对环境的适应性,为该地区植被的恢复和重建提供理论依据。结果表明：①叶性状存在种间差异且变异程度不同,变异范围为14.11%~47.63%,叶绿素含量（ChlC）变异系数最大,叶片全氮含量（LCC）变异系数最小。②叶干物质含量（LDMC）与ChlC、LCC均呈极显著正相关（P＜0.01）,ChlC与LCC呈极显著正相关（P＜0.01）,其他叶性状间相关性不显著。③不同功能群植物叶性状存在显著差异。其中,豆科植物叶片LDMC、ChlC、LCC极显著高于藜科植物（P＜0.01）。草本植物叶片比叶面积（SLA）极显著高于灌木植物叶片（P＜0.01）。一年生植物叶片SLA、LNC显著高于多年生植物（P＜0.05）;多年生植物叶片LDMC极显著高于一年生植物（P＜0.01）;多年生植物叶片C含量显著高于一年生植物（P＜0.05）。C₃植物叶片LDMC、ChlC显著高于C₄植物（P＜0.05）;C₄植物叶片δ¹³C极显著高于C₃植物 （P＜0.01）;C₃植物叶片LCC极显著（P＜0.01）高于C₄植物。     

枇杷叶片性状与单果质量的遗传规律研究

为了解枇杷(Eriobotrya japonica)叶片性状和单果质量的遗传多样性及其相关性,对‘宁海白’与‘大房’杂交组合的F₁群体(123株)的7个叶片性状与单果质量进行相关分析。结果表明,叶片的长度、宽度、厚度和叶柄长度及单果质量5个性状在后代中均呈现连续性较好的正态分布,其中单果质量、叶片的长度、宽度和厚度呈趋小遗传趋势,叶柄长度呈趋中变异趋势。F₁杂交群体叶面形态主要以“稍皱”为主,叶片形状以“椭圆形”为主,叶基形状以“楔形”为主。单果质量与叶柄长度、叶片长度、叶片宽度、叶片厚度均表现出极显著的正相关性。因此,叶柄长度可考虑作为早期筛选大果优株的参考指标之一。     

Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits

Genome-wide association studies have been successful in identifying genes involved in polygenic traits and are valuable for crop improvement. Tomato (Solanum lycopersicum) is a major crop and is highly appreciated worldwide for its health value. We used a core collection of 163 tomato accessions composed of S. lycopersicum, S. lycopersicum var cerasiforme, and Solanum pimpinellifolium to map loci controlling variation in fruit metabolites. Fruits were phenotyped for a broad range of metabolites, including amino acids, sugars, and ascorbate. In parallel, the accessions were genotyped with 5,995 single-nucleotide polymorphism markers spread over the whole genome. Genome-wide association analysis was conducted on a large set of metabolic traits that were stable over 2 years using a multilocus mixed model as a general method for mapping complex traits in structured populations and applied to tomato. We detected a total of 44 loci that were significantly associated with a total of 19 traits, including sucrose, ascorbate, malate, and citrate levels. These results not only provide a list of candidate loci to be functionally validated but also a powerful analytical approach for finding genetic variants that can be directly used for crop improvement and deciphering the genetic architecture of complex traits.In crops, linkage mapping has proved invaluable for detecting quantitative trait loci (QTLs) for traits of interest and to unravel their underlying genetic architecture. This approach is based on the analysis of the segregation of polymorphism between the parental lines and their progeny. However, one of the limitations of this approach is the reduced number of recombination events that occur per generation (for review, see Korte and Farlow, 2013). This leads to extended linkage blocks that reduce the accuracy of the linkage mapping. An alternative to linkage-based mapping studies is to perform linkage disequilibrium (LD) mapping in a population of theoretically unrelated individuals. The ancestral polymorphism segregating through this population (or panel) is far more informative compared with the polymorphism of the parental lines of the linkage mapping population (Mauricio, 2001). LD mapping, also known as genome-wide association (GWA), relies on the natural patterns of LD in the population investigated. The aim of GWA is to reveal trait-associated loci by taking advantage of the level of LD. Depending on the decay of LD, the mapping resolution can be narrowed from a large genomic portion where the level of LD is relatively high to a single marker when the LD level is very low.Following domestication, crops are prone to (1) increased levels of LD, (2) population structure (remote common ancestry of large groups of individuals), and (3) cryptic relatedness (the presence of close relatives in a sample of unrelated individuals; Riedelsheimer et al., 2012). Population structure and cryptic relatedness may lead to false-positive association in GWA studies (Astle and Balding, 2009), but their effect is now relatively well accounted for in mixed linear models (for review, see Sillanpää, 2011; Listgarten et al., 2012). The problem of high LD in GWA scans also must be taken into account: Segura et al. (2012) investigated this difficulty by proposing a multilocus mixed model (MLMM) that handles the confounding effect of background loci that may be present throughout the genome due to LD. This approach revealed multiple loci in LD and associated with sodium concentration in leaves in Arabidopsis (Arabidopsis thaliana), while previous methods failed to identify this complex pattern (Segura et al., 2012).In parallel, the development of cost-effective high-throughput sequencing technologies has identified increasingly dense variant loci necessary to conduct GWA scans, especially in model species such as rice (Oryza sativa) for agronomic traits (Huang et al., 2010) or maize (Zea mays) for drought tolerance (Lu et al., 2010; for review, see Soto-Cerda and Cloutier, 2012). However, GWA is not restricted to model species and is becoming increasingly widespread in nonmodel ones such as sunflower (Helianthus annuus; Mandel et al., 2013) and tomato (Solanum lycopersicum; Xu et al., 2013), where numerous associations have been successfully identified for traits related to plant architecture (branching in the case of sunflower) and fruit quality (e.g. fresh weight in tomato).Tomato is a crop of particular interest, as the fruit are an important source of fiber and nutrients in the human diet and a model for the study of fruit development (Giovannoni, 2001). Over the last two decades, numerous QTLs have been identified for traits such as fresh weight using linkage approaches (Frary et al., 2000; Zhang et al., 2012; Chakrabarti et al., 2013) but also for other fruit-related traits such as fruit ascorbic acid levels (Stevens et al., 2007), sensory and instrumental quality traits (Causse et al., 2002), sugar and organic acids (Fulton et al., 2002), and metabolic components (Schauer et al., 2008). Large tomato germplasm collections have been characterized at the molecular level using simple sequence repeat (Ranc et al., 2008) and single-nucleotide polymorphism (SNP) markers (Blanca et al., 2012; Shirasawa et al., 2013), giving insights into population structure, tomato evolutionary history, and the genetic architecture of traits of agronomic interest. These screens of nucleotide diversity were made possible (for review, see Bauchet and Causse, 2012) in the last couple of years due to the release of the tomato genome sequence (Tomato Genome Consortium, 2012) and derived genomic tools such as a high-density SNP genotyping array (Sim et al., 2012). The combination of large germplasm collections, high-throughput genomic tools, and traits of economic interest provide a framework to apply genome-wide association study (GWAS) in this species. In tomato, previous association studies have been limited to a targeted region (e.g. chromosome 2; Ranc et al., 2012), used low-density genome-wide-distributed SNP markers (Xu et al., 2013), or investigated a limited number of agronomic traits with low precision on the association panel (Shirasawa et al., 2013).Using tomato as a model, we aimed to investigate the genetic architecture of traits related to fruit metabolic composition at high resolution. To reach this objective, we carried out an investigation into LD patterns at the genome-wide scale and a GWA scan using the MLMM approach. We present results on the genetic architecture of fruit metabolic composition for metabolites such as organic acids, amino acids, sugars, and ascorbate in tomato.     

Mapping QTL for Grain Yield and Plant Traits in a Tropical Maize Population

The vast majority of reported QTL mapping for maize (Zea mays L.) traits are from temperate germplasm and, also, QTL by environment interaction (QTL × E) has not been thoroughly evaluated and analyzed in most of these papers. The maize growing areas in tropical regions are more prone to environmental variability than in temperate areas, and, therefore, genotype by environment interaction is of great concern for maize breeders. The objectives of this study were to map QTL and to test their interaction with environments for several traits in a tropical maize population. Two-hundred and fifty-six F_2:3 families evaluated in five environments, a genetic map with 139 microsatellites markers, and the multiple-environment joint analysis (mCIM) were used to map QTL and to test QTL × E interaction. Sixteen, eight, six, six, nine, and two QTL were mapped for grain yield, ears per plant, plant lodging, plant height, ear height, and number of leaves, respectively. Most of these QTL interacted significantly with environments, most of them displayed overdominance for all traits, and genetic correlated traits had a low number of QTL mapped in the same genomic regions. Few of the QTL mapped had already been reported in both temperate and tropical germplasm. The low number of stable QTL across environments imposes additional challenges to design marker-assisted selection in tropical areas, unless the breeding programs could be directed towards specific target areas.     

Leaf Lateral Asymmetry in Morphological and Physiological Traits of Rice Plant

Leaf lateral asymmetry in width and thickness has been reported previously in rice. However, the differences between the wide and narrow sides of leaf blade in other leaf morphological and physiological traits were not known. This study was conducted to quantify leaf lateral asymmetry in leaf width, leaf thickness, specific leaf weight (SLW), leaf nitrogen (N) concentration based on dry weight (Nw) and leaf area (Na), and chlorophyll meter reading (SPAD). Leaf morphological and physiological traits of the two lateral halves of the top three leaves at heading stage were measured on 23 rice varieties grown in three growing seasons in two locations. Leaf lateral asymmetry was observed in leaf width, leaf thickness, Nw, Na, and SPAD, but not in SLW. On average, the leaf width of the wide side was about 17% higher than that of the narrow side. The wide side had higher leaf thickness than the narrow side whereas the narrow side had higher Nw, Na, and SPAD than the wide side. We conclude that the narrow side of leaf blade maintained higher leaf N status than the wide side based on all N-related parameters, which implies a possibility of leaf lateral asymmetry in photosynthetic rate in rice plant.     

Differences in Leaf Flammability,Leaf Traits and Flammability-Trait Relationships between Native and Exotic Plant Species of Dry Sclerophyll Forest

The flammability of plant leaves influences the spread of fire through vegetation. Exotic plants invading native vegetation may increase the spread of bushfires if their leaves are more flammable than native leaves. We compared fresh-leaf and dry-leaf flammability (time to ignition) between 52 native and 27 exotic plant species inhabiting dry sclerophyll forest. We found that mean time to ignition was significantly faster in dry exotic leaves than in dry native leaves. There was no significant native-exotic difference in mean time to ignition for fresh leaves. The significantly higher fresh-leaf water content that was found in exotics, lost in the conversion from a fresh to dry state, suggests that leaf water provides an important buffering effect that leads to equivalent mean time to ignition in fresh exotic and native leaves. Exotic leaves were also significantly wider, longer and broader in area with significantly higher specific leaf area–but not thicker–than native leaves. We examined scaling relationships between leaf flammability and leaf size (leaf width, length, area, specific leaf area and thickness). While exotics occupied the comparatively larger and more flammable end of the leaf size-flammability spectrum in general, leaf flammability was significantly correlated with all measures of leaf size except leaf thickness in both native and exotic species such that larger leaves were faster to ignite. Our findings for increased flammability linked with larger leaf size in exotics demonstrate that exotic plant species have the potential to increase the spread of bushfires in dry sclerophyll forest.     

Epistatic Association Mapping for Alkaline and Salinity Tolerance Traits in the Soybean Germination Stage

Soil salinity and alkalinity are important abiotic components that frequently have critical effects on crop growth, productivity and quality. Developing soybean cultivars with high salt tolerance is recognized as an efficient way to maintain sustainable soybean production in a salt stress environment. However, the genetic mechanism of the tolerance must first be elucidated. In this study, 257 soybean cultivars with 135 SSR markers were used to perform epistatic association mapping for salt tolerance. Tolerance was evaluated by assessing the main root length (RL), the fresh and dry weights of roots (FWR and DWR), the biomass of seedlings (BS) and the length of hypocotyls (LH) of healthy seedlings after treatments with control, 100 mM NaCl or 10 mM Na₂CO₃ solutions for approximately one week under greenhouse conditions. A total of 83 QTL-by-environment (QE) interactions for salt tolerance index were detected: 24 for LR, 12 for FWR, 11 for DWR, 15 for LH and 21 for BS, as well as one epistatic QTL for FWR. Furthermore, 86 QE interactions for alkaline tolerance index were found: 17 for LR, 16 for FWR, 17 for DWR, 18 for LH and 18 for BS. A total of 77 QE interactions for the original trait indicator were detected: 17 for LR, 14 for FWR, 4 for DWR, 21 for LH and 21 for BS, as well as 3 epistatic QTL for BS. Small-effect QTL were frequently observed. Several soybean genes with homology to Arabidopsis thaliana and soybean salt tolerance genes were found in close proximity to the above QTL. Using the novel alleles of the QTL detected above, some elite parental combinations were designed, although these QTL need to be further confirmed. The above results provide a valuable foundation for fine mapping, cloning and molecular breeding by design for soybean alkaline and salt tolerance.     

QTL Mapping for Plant Architecture Traits in Upland Cotton Using RILs and SSR Markers

Xiangzamian 2 (XZM2) is the most widely cultivated cotton hybrid in China. By crossing two parents Zhongmiansuo 12 and 8891 and upon subsequent selfings, we got F₈ and F₉ populations having 180 recombinant inbred lines. Ten plant architecture traits were investigated in two years with this population. A genetic map was constructed mainly with SSR markers. Quantitative trait loci (QTL) conditioning plant architecture traits were determined at the single-locus and double-locus levels. The results showed that epistastic effects as well as additive effects of QTL played an important role as the genetic basis of cotton plant architecture. The QTL detected in our research might provide new information on improving plant architecture traits. The polymorphism of molecular markers between ZMS12 and 8891 were quite limited, while significant differences between their phenotypes were found and the hybrid XZM2 expressed high heterosis in yield. All these could be partly explained by the effect of epistatic QTL.     

利用重组自交系和SSR标记进行陆地棉株型QTL的鉴定和定位

通过中棉所12与8891的杂交及多代自交,获得由180个家系构成的重组自交系F8、F9群体。重组自交系群体、两亲本及F1于2002、2003两年种植;对株型性状进行了研究,两年共调查了10个株型形状。利用该重组自交系群体,采用SSR为主体的分子标记构建了遗传连锁图,并对株型性状进行了单位点和双位点水平的QTL定位。结果表明,QTL加性效应和上位性互作效应作为棉花重组自交系株型性状的遗传基础起着重要作用;中棉所12与8891间多态性位点偏少,而表型差异较大且其杂交种湘杂棉二号有很强的杂种优势,QTL互作可部分解释这一现象：结合对产量品质性状的研究结果,认为上位性可能是湘杂棉二号杂种优势的重要遗传基础。     

Exploring Potential of Pearl Millet Germplasm Association Panel for Association Mapping of Drought Tolerance Traits

A pearl millet inbred germplasm association panel (PMiGAP) comprising 250 inbred lines, representative of cultivated germplasm from Africa and Asia, elite improved open-pollinated cultivars, hybrid parental inbreds and inbred mapping population parents, was recently established. This study presents the first report of genetic diversity in PMiGAP and its exploitation for association mapping of drought tolerance traits. For diversity and genetic structure analysis, PMiGAP was genotyped with 37 SSR and CISP markers representing all seven linkage groups. For association analysis, it was phenotyped for yield and yield components and morpho-physiological traits under both well-watered and drought conditions, and genotyped with SNPs and InDels from seventeen genes underlying a major validated drought tolerance (DT) QTL. The average gene diversity in PMiGAP was 0.54. The STRUCTURE analysis revealed six subpopulations within PMiGAP. Significant associations were obtained for 22 SNPs and 3 InDels from 13 genes under different treatments. Seven SNPs associations from 5 genes were common under irrigated and one of the drought stress treatments. Most significantly, an important SNP in putative acetyl CoA carboxylase gene showed constitutive association with grain yield, grain harvest index and panicle yield under all treatments. An InDel in putative chlorophyll a/b binding protein gene was significantly associated with both stay-green and grain yield traits under drought stress. This can be used as a functional marker for selecting high yielding genotypes with ‘stay green’ phenotype under drought stress. The present study identified useful marker-trait associations of important agronomics traits under irrigated and drought stress conditions with genes underlying a major validated DT-QTL in pearl millet. Results suggest that PMiGAP is a useful panel for association mapping. Expression patterns of genes also shed light on some physiological mechanisms underlying pearl millet drought tolerance.     

茄子分子遗传图谱的构建及果实性状的QTL定位

以茄子(Solanum melongena)材料09-101-M和10TL-102-F4-1的重组自交系(RIL)为作图群体,构建总长度为991.7c M、共包含16个连锁群157个位点、平均图距为6.32 c M的遗传图谱。应用复合区间作图法(CIM),共检测到18个与茄子果实性状相关的QTLs,其中10个为主效QTLs,8个QTLs在两年两点的实验中能够被重复检测到。在所有QTLs中,控制果重的QTL fw1.1的效应值最大,为23.8%–31.6%,被定位在LG01(E09)上E25M34–E33M57b区域内;果长、果径与果重显著相关,且控制果长、果径与果重的QTL位于同一连锁群的相同区域。     

Genome-Wide Association Mapping of Root Traits in a Japonica Rice Panel

Rice is a crop prone to drought stress in upland and rainfed lowland ecosystems. A deep root system is recognized as the best drought avoidance mechanism. Genome-wide association mapping offers higher resolution for locating quantitative trait loci (QTLs) than QTL mapping in biparental populations. We performed an association mapping study for root traits using a panel of 167 japonica accessions, mostly of tropical origin. The panel was genotyped at an average density of one marker per 22.5 kb using genotyping by sequencing technology. The linkage disequilibrium in the panel was high (r²>0.6, on average, for 20 kb mean distances between markers). The plants were grown in transparent 50 cm × 20 cm × 2 cm Plexiglas nailboard sandwiches filled with 1.5 mm glass beads through which a nutrient solution was circulated. Root system architecture and biomass traits were measured in 30-day-old plants. The panel showed a moderate to high diversity in the various traits, particularly for deep (below 30 cm depth) root mass and the number of deep roots. Association analyses were conducted using a mixed model involving both population structure and kinship to control for false positives. Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04. The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion. Because several QTLs for different traits were co-localized, 51 unique loci were detected; several co-localized with meta-QTLs for root traits, but none co-localized with rice genes known to be involved in root growth. Several likely candidate genes were found in close proximity to these loci. Additional work is necessary to assess whether these markers are relevant in other backgrounds and whether the genes identified are robust candidates.     

Genome-Wide Association Mapping for Resistance to Leaf and Stripe Rust in Winter-Habit Hexaploid Wheat Landraces

Leaf rust, caused by Puccinia triticina (Pt), and stripe rust, caused by P. striiformis f. sp. tritici (Pst), are destructive foliar diseases of wheat worldwide. Breeding for disease resistance is the preferred strategy of managing both diseases. The continued emergence of new races of Pt and Pst requires a constant search for new sources of resistance. Here we report a genome-wide association analysis of 567 winter wheat (Triticum aestivum) landrace accessions using the Infinium iSelect 9K wheat SNP array to identify loci associated with seedling resistance to five races of Pt (MDCL, MFPS, THBL, TDBG, and TBDJ) and one race of Pst (PSTv-37) frequently found in the Northern Great Plains of the United States. Mixed linear models identified 65 and eight significant markers associated with leaf rust and stripe rust, respectively. Further, we identified 31 and three QTL associated with resistance to Pt and Pst, respectively. Eleven QTL, identified on chromosomes 3A, 4A, 5A, and 6D, are previously unknown for leaf rust resistance in T. aestivum.     

Genome-Wide Association Mapping for Kernel and Malting Quality Traits Using Historical European Barley Records

Malting quality is an important trait in breeding barley (Hordeum vulgare L.). It requires elaborate, expensive phenotyping, which involves micro-malting experiments. Although there is abundant historical information available for different cultivars in different years and trials, that historical information is not often used in genetic analyses. This study aimed to exploit historical records to assist in identifying genomic regions that affect malting and kernel quality traits in barley. This genome-wide association study utilized information on grain yield and 18 quality traits accumulated over 25 years on 174 European spring and winter barley cultivars combined with diversity array technology markers. Marker-trait associations were tested with a mixed linear model. This model took into account the genetic relatedness between cultivars based on principal components scores obtained from marker information. We detected 140 marker-trait associations. Some of these associations confirmed previously known quantitative trait loci for malting quality (on chromosomes 1H, 2H, and 5H). Other associations were reported for the first time in this study. The genetic correlations between traits are discussed in relation to the chromosomal regions associated with the different traits. This approach is expected to be particularly useful when designing strategies for multiple trait improvements.     

Genome-Wide Association Mapping of Yield and Grain Quality Traits in Winter Wheat Genotypes

The main goal of this study was to investigate the genetic basis of yield and grain quality traits in winter wheat genotypes using association mapping approach, and identify linked molecular markers for marker assisted selection. A total of 120 elite facultative/winter wheat genotypes were evaluated for yield, quality and other agronomic traits under rain-fed and irrigated conditions for two years (2011–2012) at the Tel Hadya station of ICARDA, Syria. The same genotypes were genotyped using 3,051 Diversity Array Technologies (DArT) markers, of which 1,586 were of known chromosome positions. The grain yield performance of the genotypes was highly significant both in rain-fed and irrigated sites. Average yield of the genotypes ranged from 2295 to 4038 kg/ha and 4268 to 7102 kg/ha under rain-fed and irrigated conditions, respectively. Protein content and alveograph strength (W) ranged from 13.6–16.1% and 217.6–375 Jx10-4, respectively. DArT markers wPt731910 (3B), wPt4680 (4A), wPt3509 (5A), wPt8183 (6B), and wPt0298 (2D) were significantly associated with yield under rain-fed conditions. Under irrigated condition, tPt4125 on chromosome 2B was significantly associated with yield explaining about 13% of the variation. Markers wPt2607 and wPt1482 on 5B were highly associated with protein content and alveograph strength explaining 16 and 14% of the variations, respectively. The elite genotypes have been distributed to many countries using ICARDA’s International system for potential direct release and/or use as parents after local adaptation trials by the NARSs of respective countries. The QTLs identified in this study are recommended to be used for marker assisted selection after through validation using bi-parental populations.     

Quantitative Trait Loci Mapping of Leaf Morphological Traits and Chlorophyll Content in Cultivated Tetraploid Cotton

Genetic mapping provides a powerful tool for quantitative trait loci （QTL） analysis at the molecular level. A simple sequence repeat （SSR） genetic map containing 590 markers and a BCI population from two cultivated tetraploid cotton （Gossypium hirsutum L.） cultivars, namely TM-1 and Hai 7124 （G. barbadense L.）, were used to map and analyze QTL using the composite interval mapping （CIM） method. Thirty one QTLs, 10 for lobe length, 13 for lobe width, six for lobe angle, and two for leaf chlorophyll content, were detected on 15 chromosomes or linkage groups at logarithm of odds （LOD）≥2.0, of which 15 were found for leaf morphology at LOD≥3.0. The genetic effects of the QTL were estimated. These results are fundamental for marker-assisted selection （MAS） of these traits in tetraploid cotton breeding.     

Association Mapping across Numerous Traits Reveals Patterns of Functional Variation in Maize

Phenotypic variation in natural populations results from a combination of genetic effects, environmental effects, and gene-by-environment interactions. Despite the vast amount of genomic data becoming available, many pressing questions remain about the nature of genetic mutations that underlie functional variation. We present the results of combining genome-wide association analysis of 41 different phenotypes in ∼5,000 inbred maize lines to analyze patterns of high-resolution genetic association among of 28.9 million single-nucleotide polymorphisms (SNPs) and ∼800,000 copy-number variants (CNVs). We show that genic and intergenic regions have opposite patterns of enrichment, minor allele frequencies, and effect sizes, implying tradeoffs among the probability that a given polymorphism will have an effect, the detectable size of that effect, and its frequency in the population. We also find that genes tagged by GWAS are enriched for regulatory functions and are ∼50% more likely to have a paralog than expected by chance, indicating that gene regulation and gene duplication are strong drivers of phenotypic variation. These results will likely apply to many other organisms, especially ones with large and complex genomes like maize.     

RFLP Mapping in Soybean: Association between Marker Loci and Variation in Quantitative Traits

Quantitative trait loci (QTLs) have been mapped to small intervals along the chromosomes of tomato (Lycopersicon esculentum), by a method we call substitution mapping. The size of the interval to which a QTL can be mapped is determined primarily by the number and spacing of previously mapped genetic markers in the region surrounding the QTL. We demonstrate the method using tomato genotypes carrying chromosomal segments from Lycopersicon chmielewskii, a wild relative of tomato with high soluble solids concentration but small fruit and low yield. Different L. chmielewskii chromosomal segments carrying a common restriction fragment length polymorphism were identified, and their regions of overlap determined using all available genetic markers. The effect of these chromosomal segments on soluble solids concentration, fruit mass, yield, and pH, was determined in the field. Many overlapping chromosomal segments had very different phenotypic effects, indicating QTLs affecting the phenotype(s) to lie in intervals of as little as 3 cM by which the segments differed. Some associations between different traits were attributed to close linkage between two or more QTLs, rather than pleiotropic effects of a single QTL: in such cases, recombination should separate desirable QTLs from genes with undesirable effects. The prominence of such trait associations in wide crosses appears partly due to infrequent reciprocal recombination between heterozygous chromosomal segments flanked by homozygous regions. Substitution mapping is particularly applicable to gene introgression from wild to domestic species, and generally useful in narrowing the gap between linkage mapping and physical mapping of QTLs.