There is more to tomato fruit colour than candidate carotenoid genes

Determining gene sequences responsible for complex phenotypes has remained a major objective in modern biology. The candidate gene approach is attempting to link, through mapping analysis, sequences that have a known functional role in the measured phenotype with quantitative trait loci (QTL) that are responsible for the studied variation. To explore the potential of the candidate approach for complex traits we conducted a mapping analysis of QTL for the intensity of the red colour of the tomato fruit (mainly lycopene) and for probes associated with the well-characterized carotenoid biosynthesis pathway. Seventy-five tomato introgression lines (ILs), each containing a single homozygous RFLP-defined chromosome segment from the green-fruited species Lycopersicon pennellii delimited 107 marker-defined mapping bins. Three of the bins resolved known qualitative colour mutations for yellow (r) and orange (B and Del) fruits resulting from variation in specific carotenoid biosynthesis genes. Based on trials in different environments, 16 QTL that modified the intensity of the red colour of ripe fruit were assigned to bins. Candidate sequences associated with the carotenoid biosynthesis pathway were mapped to 23 loci. Only five of the QTL co-segregated with the same bins that contained candidate genes - a number that is expected by chance alone. Furthermore, similar map location of a QTL and a candidate is far from a direct causative relationship between a gene and a phenotype. This study highlights the wealth and complexity of the variation present in the genus Lycopersicon that could be employed for basic research and genetic improvement of fruit colour in tomato.     

一个获得与缺失变异(PAV)调控甜瓜果实苦味

甜瓜苦味物质严重影响其口感和品质。本研究利用不苦的薄皮甜瓜品系C69和苦的薄皮甜瓜品系C14构建了一个包含100个单株的F2群体。首先利用2b-RAD测序构建一个遗传连锁图谱。其次,结合群体的苦味性状进行全基因组的QTL定位和关联分析。然后,利用2b-RAD测序特有的技术优势进行群体的获得与缺失变异(PAV)的挖掘。最后,利用亲本的重测序信息确定控制苦味性状的关键基因。结果发现,F1的果实表现出强烈的苦味,F2群体中苦与不苦的单株分别为81个和19个,符合3∶1的分离比(χ^2=1.92,P=0.1659),表型表明所用甜瓜材料的苦味主要是由一个显性的基因位点控制。利用477个SNP标记构建一张包含10个连锁群的连锁图谱,总长为337.79 cM,标记间平均间隔0.71 cM。全基因组QTL定位在8号连锁群(对应9号染色体),检测到一个解释表型变异为20%的甜瓜苦味QTL。全基因组关联分析检测到7个SNPs与苦味性状相关,全部位于9号染色体苦味QTL的基因组区域。通过PAV分型分析仅发现一个特有的大片段缺失(21707702~21743072 bp),位于QTL区域,且在所有的不苦株系中存在,而苦的株系中不存在。基于两个亲本材料的深度重测序信息,发现这个PAV的区域更大,约为62 Kb,共涉及到9个连续的基因(MELO3C005601、MELO3C005602、MELO3C005603、MELO3C005604、MELO3C005605、MELO3C005606、MELO3C005607、MELO3C005608和MELO3C005609),其中5个是细胞色素P450基因。构建的系统发育树表明,这5个细胞色素P450基因与参与葫芦素C/B/E合成的细胞色素P450基因簇CYP81Q58、CYP81Q59和CYP712D8在一个进化枝,可能行使类似的功能,为潜在的类似于黄瓜葫芦素C合成的基因簇的一部分。前人通过比较基因组学研究获得的2个控制葫芦素B合成的bHLH转录因子CmBr(MELO3C005610)和CmBt(MELO3C005611)同在9号染色体,与本研究检测到的PAV紧密挨在一起。我们的研究结果为后续不苦甜瓜的育种提供了新的理论支撑和分子辅助育种目标。     

Fruit carbohydrate metabolism in an introgression line of tomato with increased fruit soluble solids

A tomato line (IL9-2-5) of the cultivated species, Lycopersicon esculentum, carrying a 9 cM introgression from the wild species, Lycopersicon pennelli, produces fruit with high soluble solids content (Brix), an important determinant of fruit quality for processing. Two quantitative trait loci (QTLs) relating to fruit soluble solids content have been identified within the introgressed segment. One of these QTLs (PW-9-2-5) is silent under the growth conditions used in this study, while a second (Brix-9-2-5) has been shown to encode a fruit apoplastic invertase (Lin5) with altered kinetic properties. In this study, we have undertaken a detailed biochemical analysis of the introgression line to attempt to gain an understanding of the metabolic changes associated with increased fruit soluble solids. Increased Brix in ripe fruit was shown to be the result of increased sucrose and glucose, with a more minor contribution from aspartate and alanine. The introgression leads to a pronounced increase in apoplastic invertase activity in the columella tissue that extends throughout fruit development. Furthermore, columella tissue from IL9-2-5 fruit has a greater capacity to take up exogenously supplied sucrose, an observation that is consistent with the kinetic properties of the introgressed Lin5 allele. Apart from the increase in mature fruit sugar and increases in some amino acids, metabolite profiling revealed few other metabolic perturbations in fruit from IL9-2-5. The only other major change was a dramatic increase in starch accumulation at earlier stages of fruit metabolism. This occurred without any increase in the activity of the enzymes of sucrose metabolism or starch synthesis and may therefore be driven by increased availability of sucrose. We conclude that the major factor that leads to increased fruit sugar in IL9-2-5 is an increase in the capacity to take up sucrose unloaded from the phloem.     

Fine mapping, phenotypic characterization and validation of non-race-specific resistance to powdery mildew in a wheat–Triticum militinae introgression line

Introgression of several genomic loci from tetraploid Triticum militinae into bread wheat cv. T?hti has increased resistance of introgression line 8.1 to powdery mildew in seedlings and adult plants. In our previous work, only a major quantitative trait locus (QTL) on chromosome 4AL of the line 8.1 contributed significantly to resistance, whereas QTL on chromosomes 1A, 1B, 2A, 5A and 5B were detected merely on a suggestive level. To verify and characterize all QTLs in the line 8.1, a mapping population of double haploid lines was established. Testing for seedling resistance to 16 different races/mixtures of Blumeria graminis f. sp. tritici revealed four highly significant non-race-specific resistance QTL including the main QTL on chromosome 4AL, and a race-specific QTL on chromosome 5B. The major QTL on chromosome 4AL (QPm.tut-4A) as well as QTL on chromosome 5AL and a newly detected QTL on 7AL were highly effective at the adult stage. The QPm.tut-4A QTL accounts on average for 33-49 % of the variation in resistance in the double haploid population. Interactions between the main QTL QPm.tut-4A and the minor QTL were evaluated and discussed. A population of 98 F(2) plants from a cross of susceptible cv. Chinese Spring and the line 8.1 was created that allowed mapping the QPm.tut-4A locus to the proximal 2.5-cM region of the introgressed segment on chromosome 4AL. The results obtained in this work make it feasible to use QPm.tut-4A in resistance breeding and provide a solid basis for positional cloning of the major QTL.     

DNA variation at the invertase locus invGE/GF is associated with tuber quality traits in populations of potato breeding clones

Starch and sugar content of potato tubers are quantitative traits, which are models for the candidate gene approach for identifying the molecular basis of quantitative trait loci (QTL) in noninbred plants. Starch and sugar content are also important for the quality of processed products such as potato chips and French fries. A high content of the reducing sugars glucose and fructose results in inferior chip quality. Tuber starch content affects nutritional quality. Functional and genetic models suggest that genes encoding invertases control, among other things, tuber sugar content. The invGE/GF locus on potato chromosome IX consists of duplicated invertase genes invGE and invGF and colocalizes with cold-sweetening QTL Sug9. DNA variation at invGE/GF was analyzed in 188 tetraploid potato cultivars, which have been assessed for chip quality and tuber starch content. Two closely correlated invertase alleles, invGE-f and invGF-d, were associated with better chip quality in three breeding populations. Allele invGF-b was associated with lower tuber starch content. The potato invertase gene invGE is orthologous to the tomato invertase gene Lin5, which is causal for the fruit-sugar-yield QTL Brix9-2-5, suggesting that natural variation of sugar yield in tomato fruits and sugar content of potato tubers is controlled by functional variants of orthologous invertase genes.     

An integrated view of quantitative trait variation using tomato interspecific introgression lines

Resolving natural phenotypic variation into genetic and molecular components is a major objective in biology. Over the past decade, tomato interspecific introgression lines (ILs), each carrying a single 'exotic' chromosome segment from a wild species, have exposed thousands of quantitative trait loci (QTL) affecting plant adaptation, morphology, yield, metabolism, and gene expression. QTL for fruit size and sugar composition were isolated by map-based cloning, while others were successfully implemented in marker-assisted breeding programs. More recently, integrating the multitude of IL-QTL into a single database has unraveled some unifying principles about the architecture of complex traits in plants.     

QTL Mapping of Low-Temperature Germination Ability in the Maize IBM Syn4 RIL Population

Low temperature is the primary factor to affect maize sowing in early spring. It is, therefore, vital for maize breeding programs to improve tolerance to low temperatures at seed germination stage. However, little is known about maize QTL involved in low-temperature germination ability. 243 lines of the intermated B73×Mo17 (IBM) Syn4 recombinant inbred line (RIL) population was used for QTL analysis of low-temperature germination ability. There were significant differences in germination-related traits under both conditions of low temperature (12°C/16h, 18°C/8h) and optimum temperature (28°C/24h) between the parental lines. Only three QTL were identified for controlling optimum-temperature germination rate. Six QTL controlling low-temperature germination rate were detected on chromosome 4, 5, 6, 7 and 9, and contribution rate of single QTL explained between 3.39%~11.29%. In addition, six QTL controlling low-temperature primary root length were detected in chromosome 4, 5, 6, and 9, and the contribution rate of single QTL explained between 3.96%~8.41%. Four pairs of QTL were located at the same chromosome position and together controlled germination rate and primary root length under low temperature condition. The nearest markers apart from the corresponding QTL (only 0.01 cM) were umc1303 (265.1 cM) on chromosome 4, umc1 (246.4 cM) on chromosome 5, umc62 (459.1 cM) on chromosome 6, bnl14.28a (477.4 cM) on chromosome 9, respectively. A total of 3155 candidate genes were extracted from nine separate intervals based on the Maize Genetics and Genomics Database (http://www.maizegdb.org). Five candidate genes were selected for analysis as candidates putatively affecting seed germination and seedling growth at low temperature. The results provided a basis for further fine mapping, molecular marker assisted breeding and functional study of cold-tolerance at the stage of seed germination in maize.     

Refinement of two female fertility QTL using alternative phenotypes in French Holstein dairy cattle

Two quantitative trait loci (QTL) affecting female fertility were mapped in French dairy cattle. Phenotypes were non-return rates at 28, 56, 90 and 282 days after insemination. On chromosome 3, a QTL was significant at 1% for non-return rate at 90 days, suggesting that it affects early fertility events. An analysis of SLC35A3, which causes complex vertebral malformation, excluded this gene from the QTL interval. On chromosome 7, a QTL was almost significant (P = 0.05) for non-return rate at 282 days. This QTL was associated with abortion and stillbirth problems. Use of appropriate phenotypes appeared important for fine-mapping QTL associated with fertility.     

Quantitative trait loci mapping in F(2) crosses between outbred lines

We develop a mixed-model approach for QTL analysis in crosses between outbred lines that allows for QTL segregation within lines as well as for differences in mean QTL effects between lines. We also propose a method called "segment mapping" that is based in partitioning the genome in a series of segments. The expected change in mean according to percentage of breed origin, together with the genetic variance associated with each segment, is estimated using maximum likelihood. The method also allows the estimation of differences in additive variances between the parental lines. Completely fixed random and mixed models together with segment mapping are compared via simulation. The segment mapping and mixed-model behaviors are similar to those of classical methods, either the fixed or random models, under simple genetic models (a single QTL with alternative alleles fixed in each line), whereas they provide less biased estimates and have higher power than fixed or random models in more complex situations, i.e., when the QTL are segregating within the parental lines. The segment mapping approach is particularly useful to determining which chromosome regions are likely to contain QTL when these are linked.     

Quantitative trait locus analysis of atherosclerosis in an intercross between C57BL/6 and C3H mice carrying the mutant apolipoprotein E gene

Inbred mouse strains C57BL/6J (B6) and C3H/HeJ (C3H) differ significantly in atherosclerosis susceptibility and plasma lipid levels on the apolipoprotein E-deficient (apoE-/-) background when fed a Western diet. To determine genetic factors contributing to the variations in these phenotypes, we performed quantitative trait locus (QTL) analysis using an intercross between the two strains carrying the apoE-/- gene. Atherosclerotic lesions at the aortic root and plasma lipid levels of 234 female F2 mice were analyzed after being fed a Western diet for 12 weeks. QTL analysis revealed one significant QTL, named Ath22 (42 cM, LOD 4.1), on chromosome 9 and a suggestive QTL near D11mit236 (20 cM, LOD 2.4) on chromosome 11 that influenced atherosclerotic lesion size. One significant QTL on distal chromosome 1, which accounted for major variations in plasma LDL/VLDL cholesterol and triglyceride levels, coincided with a QTL having strong effects on body weight. Plasma LDL/VLDL cholesterol or triglyceride levels of F2 mice were significantly correlated with body weight, but they were not correlated with atherosclerotic lesion sizes. These data indicate that atherosclerosis susceptibility and plasma cholesterol levels are controlled by separate genetic factors in the B6 and C3H mouse model and that genetic linkages exist between body weight and lipoprotein metabolism.     

Characterization of QTL for oil content in maize kernel

Kernel oil content in maize is a complex quantitative trait. Phenotypic variation in kernel oil content can be dissected into its component traits such as oil metabolism and physical characteristics of the kernel, including embryo size and embryo-to-endosperm weight ratio (EEWR). To characterize quantitative trait loci (QTL) for kernel oil content, a recombinant inbred population derived from a cross between normal line B73 and high-oil line By804 was genotyped using 228 molecular markers and phenotyped for kernel oil content and its component traits [embryo oil content, embryo oil concentration, EEWR, embryo volume, embryo width, embryo length, and embryo width-to-length ratio (EWLR)]. A total of 58 QTL were identified for kernel oil content and its component traits in 26 genomic regions across all chromosomes. Eight main-effect QTL were identified for kernel oil content, embryo oil content, embryo oil concentration, EEWR, embryo weight, and EWLR, each accounting for over 10?% of the phenotypic variation in six genomic regions. Over 90?% of QTL identified for kernel oil content co-localized with QTL for component traits, validating their molecular contribution to kernel oil content. On chromosome 1, the QTL that had the largest effect on kernel oil content (qKO1-1) was associated with embryo width; on chromosome 9, the QTL for kernel oil content (qKO9) was related to EEWR (qEEWR9). Embryo oil concentration and embryo width were identified as the most important component traits controlling the second largest QTL for kernel oil content on chromosome 6 (qKO6) and a minor QTL for kernel oil content on chromosome 5 (qKO5-2), respectively. The dissection of kernel oil QTL will facilitate future cloning and/or functional validation of kernel oil content, and help to elucidate the genetic basis of kernel oil content in maize.     

穗颈维管性状与产量相关性状的遗传分析

穗颈维管性状是实现"源"合成的同化物输送至籽粒中的唯一通道.本研究利用来源于籼稻93-11(受体)和粳稻日本晴(供体)构建的染色体片段代换系群体,调查穗颈维管性状与穗部产量性状.结果表明,大部分穗颈维管性状与穗部产量性状呈显著相关;7个穗颈维管性状共检测到42个QTL,其中16个位点日本晴等位基因起增效作用;6个穗部产...     

QTL analysis of falling number and seed longevity in wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.)

Pre-harvest sprouting (PHS) and seed longevity (SL) are complex biological processes of major importance for agricultural production. In the present study, a recombinant inbred line (RIL) population derived from a cross between the German winter wheat (Triticum aestivum L.) cultivars History and Rubens was used to identify genetic factors controlling these two physiological seed traits. A falling number (FN) test was employed to evaluate PHS, while SL was measured using a germination test (and the speed of germination) after controlled deterioration. FN of the population was assessed in four environments; SL traits were measured in one environment. Four major quantitative trait loci (QTL) for FN were detected on chromosomes 4D, 5A, 5D, and 7B, whereas for SL traits, a major QTL was found on chromosome 1A. The FN QTL on chromosome 4D that coincided with the position of the dwarfing gene Rht-D1b only had effects in environments that were free of PHS. The remaining three QTL for FN were mostly pronounced under conditions conducive to PHS. The QTL on the long arm of chromosome 7B corresponded to the major gene locus controlling late maturity α-amylase (LMA) in wheat. The severity of the LMA phenotype became truly apparent under sprouting conditions. The position on the long arm of chromosome 1A of the QTL for SL points to a new QTL for this important regenerative seed trait.     

Fine mapping of QTLs of chromosome 2 affecting the fruit architecture and composition of tomato

Negative correlations between quality traits and fruit size may hamper the breeding of fresh market tomato varieties for better organoleptic qualities. In a recent QTL analysis, QTLs with large effects on fruit weight, locule number and several quality traits were detected in the distal 50 cM of chromosome 2, but favorable alleles for fruit weight and locule number were unfavorable to quality traits. Substitution mapping was undertaken to determine whether the effects were due to a single QTL or to several tightly linked QTLs. Several chromosomal segments were characterized using near-isogenic lines. Five of them appeared to be involved in one or several traits. Considering the five segments from the top to the bottom of the region, the QTLs detected in each segment controlled the variation of: (1) fruit weight, (2) soluble solids content and dry matter weight, (3) fruit weight, (4) locule number and (5) fruit weight, dry matter weight, total sugars, titratable acidity and soluble solids content. This last cluster illustrates an antagonism between fruit weight and four quality traits, as favorable alleles are not conferred by the same parent in both cases. Nevertheless, several antagonistic QTLs were separated from each other in the first four segments, holding the promise for marker-assisted improvement of fruit quality traits without compromising the fruit size.     

利用RIL和CSSL群体检测水稻种子休眠性QTL

利用由梗稻品种Asominori与籼稻品种IR24的杂交组合衍生的重组自交F10。家系(Recombinant Inbred Lines,RIL)群体及其衍生的染色体片段置换系(Chromosome Segment Substitution Lines,CSSL)群体,进行了种子休眠性QTL的检测和遗传效应分析。其中CSSL群体有2个,即CSSLl(以Asominori为背景,置换片段来自IR24)和CSSL2(以IR24为背景,置换片段来自Asominori)。在RIL群体上共检测到3个种子休眠性QTL,分别位于第3、6和9染色体上;在CSSL1群体中检测到分布在第1、3和7染色体上的3个休眠性QTL;而在CSSl2群体上检测到的3个QTL则分别位于第1、2和7染色体上。同时在两套CSSL群体上,分别检测到位于第1、7染色体上位置相近且效应一致的休眠性QTL,分析表明其所在的Asominori片段含对种子休眠性的增效基因,相应的IB24段含有减效基因。     

Quantitative trait locus analysis in crosses between outbred lines with dominance and inbreeding

In an effort to determine the genetic basis of exceptionally large tomato fruits, QTL analysis was performed on a population derived from a cross between the wild species Lycopersicon pimpinellifolium (average fruit weight, 1 g) and the L. esculentum cultivar var. Giant Heirloom, which bears fruit in excess of 1000 g. QTL analysis revealed that the majority (67%) of phenotypic variation in fruit size could be attributed to six major loci localized on chromosomes 1-3 and 11. None of the QTL map to novel regions of the genome-all have been reported in previous studies involving moderately sized tomatoes. This result suggests that no major QTL beyond those already reported were involved in the evolution of extremely large fruit. However, this is the first time that all six QTL have emerged in a single population, suggesting that exceptionally large-fruited varieties, such as Giant Heirloom, are the result of a novel combination of preexisting QTL alleles. One of the detected QTL, fw2.2, has been cloned and exerts its effect on fruit size through global control of cell division early in carpel/fruit development. However, the most significant QTL detected in this study (fw11.3, lcn11.1) maps to the bottom of chromosome 11 and seems to exert its effect on fruit size through control of carpel/locule number. A second major locus, also affecting carpel number (and hence fruit size), was mapped to chromosome 2 (fw2.1, lcn2.1). We propose that these two carpel number QTL correspond to the loci described by early classical geneticists as fasciated (f) and locule number (lc), respectively.     

An Introgression Line Population of Lycopersicon Pennellii in the Cultivated Tomato Enables the Identification and Fine Mapping of Yield-Associated Qtl

Methodologies for mapping of genes underlying quantitative traits have advanced considerably but have not been accompanied by a parallel development of new population structures. We present a novel population consisting of 50 introgression lines (ILs) originating from a cross between the green-fruited species Lycopersicon pennellii and the cultivated tomato (cv M82). Each of the lines contains a single homozygous restriction fragment length polymorphism-defined L. pennellii chromosome segment, and together the lines provide complete coverage of the genome and a set of lines nearly isogenic to M82. A field trial of the ILs and their hybrids revealed at least 23 quantitative trait loci (QTL) for total soluble solids content and 18 for fruit mass; these estimates are twice as high as previously reported estimates based on traditional mapping populations. For finer mapping of a QTL affecting fruit mass, the introgressed segment was recombined into smaller fragments that allowed the identification of three linked loci. At least 16 QTL for plant weight, 22 for percentage green fruit weight, 11 for total yield and 14 for total soluble solids yield were identified. Gene action for fruit and plant characteristics was mainly additive, while overdominance (or pseudo-overdominance) of wild species introgressions was detected for yield.     

Fine mapping of a quantitative trait locus (QTL) from Lycopersicon hirsutum chromosome 1 affecting fruit characteristics and agronomic traits: breaking linkage among QTLs affecting different traits and dissection of heterosis for yield

The near-isogenic Line TA523, containing a 40-cM introgression at the bottom of chromosome 1 from Lycopersicon hirsutum acc. LA1777, affects several agronomically important traits. A set of recombinant lines (subNILs) derived from the original NIL TA523 were developed in order to fine-map, by substitution mapping, the genetic factors included within the original introgression. In the current experiment, TA523 showed redder, rounded, less pigmented shoulder, lower-weighted fruits and higher brix, whereas higher yield and brix*yield was observed only in the hybrid TA253×TA209 suggesting heterosis for these traits. By substitution mapping we mapped independent genetic loci affecting brix, yield and fruit shape, whereas fruit weight, shoulder pigmentation and external color mapped to a position coincident with the brix locus. Analysis of the subNILs revealed that the gene action of most of the QTLs was additive or nearly additive. The exception was for the yield QTL which was dominant (d/a=0.7), eliminating the possibility that yield increase is due to true overdominance at a single gene locus. However, no negative yield effects were detected in other regions of the introgressed segment, as would be predicted by a dominance complementation model. Therefore, epistatic interactions among genetic factors along the introgressed segment are suggested as the cause of yield heterosis. Results from this study, combined with previous experiments involving different tomato wild species, demonstrate that the base of chromosome 1 of tomato contains multiple QTLs affecting various agronomic and fruit traits and that these effects can not be attributed to the pleiotropic effects of a single locus. Received: 21 April 1999 / Accepted: 17 June 1999     

基于CSSL的高密度物理图谱定位水稻分蘖角度QTL

对以籼稻9311为遗传背景携带粳稻日本晴基因组的染色体片段置换系（CSSL）的遗传图谱进行分子标记加密,构建了含250个多态标记的高密度物理图谱。以119个CSSLs为材料,P≤0.001为阈值,筛选到分蘖角度与受体亲本9311差异极显著的10个系。结合物理图谱和代换作图方法,共鉴定出5个分蘖角度QTL,其中qTA11的加性效应表现为增效作用,来源于9311的等位基因;其余4个QTL的加性效应为减效作用,均来源于日本晴的等位基因。qTA6-1和qTA6-2分别被定位于第6染色体RM253–RM527之间的3.55Mb区段和RM3139–RM494的1.65Mb区间;qTA9被定位于第9染色体RM257–RM189之间的3.40Mb区段;qTA10被定位在第10染色体RM222–S10-1之间的2.10Mb区段;qTA11被定位于第11染色体RM1761–RM4504之间的3.30Mb区间。以上研究结果为水稻分蘖角度QTL的精细定位和株型育种提供了依据。