The genetic and functional analysis of flavor in commercial tomato: the FLORAL4 gene underlies a QTL for floral aroma volatiles in tomato fruit

Tomato (Solanum lycopersicum L.) has become a popular model for genetic studies of fruit flavor in the last two decades. In this article we present a study of tomato fruit flavor, including an analysis of the genetic, metabolic and sensorial variation of a collection of contemporary commercial glasshouse tomato cultivars, followed by a validation of the associations found by quantitative trait locus (QTL) analysis of representative biparental segregating populations. This led to the identification of the major sensorial and chemical components determining fruit flavor variation and detection of the underlying QTLs. The high representation of QTL haplotypes in the breeders’ germplasm suggests that there is great potential for applying these QTLs in current breeding programs aimed at improving tomato flavor. A QTL on chromosome 4 was found to affect the levels of the phenylalanine‐derived volatiles (PHEVs) 2‐phenylethanol, phenylacetaldehyde and 1‐nitro‐2‐phenylethane. Fruits of near‐isogenic lines contrasting for this locus and in the composition of PHEVs significantly differed in the perception of fruity and rose‐hip‐like aroma. The PHEV locus was fine mapped, which allowed for the identification of FLORAL4 as a candidate gene for PHEV regulation. Using a gene‐editing‐based (CRISPR‐CAS9) reverse‐genetics approach, FLORAL4 was demonstrated to be the key factor in this QTL affecting PHEV accumulation in tomato fruit.     

番茄花萼在蕾期至果实红熟期的发育形态学及其多样性研究

萼片是番茄花和果实的重要组成部分,影响着果实的商品性。本试验以40份不同类型番茄为材料,对萼片发育过程、形态描述指标及形态多样性进行研究。结果表明,番茄萼片属于宿萼,其形态随着花和果实的发育而变化,表现为闭合、微开、展开、收合、微开、变形到定形,定形萼片呈现包被、基平、上翘、直立和上卷5种状态;对定形萼片7个形态性状观测表明,变异系数由大到小依次为萼片卷曲度(84.43%)、萼片面积(45.54%)、上翘度(40.93%)、形状系数(36.05%)、萼片长(35.02%)、萼片厚(29.46%)和萼片宽(24.61%)。相关性分析表明,萼片长、萼片宽、萼片厚和萼片面积四者之间均极显著正相关;萼片形状系数(萼片长/萼片宽)与萼片长极显著正相关,而与萼片宽无显著相关关系;萼片卷曲度和上翘度之间极显著正相关,而与其他5个性状没有显著相关关系。主成分分析表明,由萼片长、萼片宽、萼片厚和萼片面积代表的大小性状(PC1),由形状系数代表的形状性状(PC2),以及由卷曲度和上翘度代表的形态性状(PC3)3个主成分对萼片形态变异的累计贡献率达87.50%;用形态性状指标对定形的5种类型萼片形态进行了描述。     

一个新的番茄黄绿叶突变体表型鉴定与遗传分析

植物黄绿叶突变体不但在植物的光合作用、叶绿素的合成代谢途径、叶绿体的遗传分化与发育等一系列基础研究中具有重要作用,而且还可以作为标记性状应用到育种研究上。本研究以前期化学诱变得到的一个番茄黄绿叶突变体为材料,对其主要表型与光合作用特征特性进行鉴定分析,发现突变体从第1片真叶开始变黄,植株矮小,叶片叶绿素含量和净光合速率相对野生型极显著降低,叶绿体类囊体片层结构畸形。突变体和野生型进行正反交,分析其遗传方式。发现其F2群体正常叶与黄绿叶的分离比为3∶1,表明黄绿叶是由单个基因突变引起的隐性性状。本研究为后期的基因定位研究奠定了基础。     

Moving from QTL experimental results to the utilization of QTL in breeding programmes

Results from quantitative trait loci studies cannot be readily implemented into breeding schemes through marker assisted selection because of uncertainty about whether the quantitative trait loci identified are real and whether the identified quantitative trait loci are segregating in the breeding population. The present paper outlines and discusses strategies to reduce uncertainty in the results from quantitative trait loci studies. One strategy to confirm results from quantitative trait loci studies is to combine P -values from many quantitative trait loci experiments, while another is to establish a confirmation study. The power of a confirmation study must be high to ensure that the postulated quantitative trait loci can be verified. In the calculation of the experimental power, there are many issues that have to be addressed: size of the quantitative trait loci to be detected, significance level required, experimental design and expected heterozygosity for the design. To ensure marker assisted selection can be quickly implemented once quantitative trait loci are confirmed, DNA samples should be retained from daughters, and the sires and dams of elite sires.     

Changes in growth and activity of enzymes involved in nitrate reduction and ammonium assimilation in tomato seedlings in response to NaCl stress

BACKGROUND AND AIMS: In Tunisia, salt water is largely used for tomato irrigation. In this work, a study was made of the changes in the nitrate reduction and ammonium assimilation into amino acids in tomato seedlings under salinity in order to providee further insight into the salt effects on plant growth. Methods Ten-day-old tomatoes (Solanum lycopersicum) were subjected to 100 mm NaCl stress, and nitrogen metabolism in leaves and roots was studied. KEY RESULTS: The concentrations of Na+ and Cl- rapidly increased in the leaves and in the roots following exposure of tomato seedlings to NaCl stress. In contrast, the NO3- concentrations were lowered first in the roots and later in the leaves. From 5 to 10 d of treatment, salt ions provoked a decrease in the dry weight and an increase in the NH4+ concentrations in the leaves. Inhibition was observed in the leaves for the activities of nitrate reductase (NR, EC 1.6.6.1), ferredoxin-dependent glutamate synthase (Fd-GOGAT, EC 1.4.7.1) and deaminating glutamate dehydrogenase (NAD-GDH, EC 1.4.1.2). NaCl affected these enzyme activities less in the roots than in leaves. This was in accordance with the pronounced decrease of dry weight by salt in leaves compared with that in the roots. CONCLUSIONS: NaCl stress effects on growth, metabolite concentrations and enzyme activities depended on the duration of salt treatment and the plant tissue.     

Reducing the interval of a growth QTL on chromosome 4 in laying hens

In our previous research, we identified a QTL with an interval of 3.4 Mb for growth on chicken chromosome (GGA) 4 in an advanced intercross population of an initial cross between the New Hampshire inbred line (NHI) and the White Leghorn inbred line (WL77). In the current study, an association analysis was performed in a population of purebred white layers (WLA) with White Leghorn origin. Genotypic data of 130 SNPs within the previously identified 3.4‐Mb region were obtained using a 60K SNP chip. In total, 24 significant SNPs (LOD ≥ 4.44) on GGA4 were detected for daily weigh gain from 8 to 14 weeks and two SNPs (LOD ≥ 4.80) for body weight at 14 weeks. The QTL interval was reduced by 1.9 Mb to an interval of 1.5 Mb (74.6–76.1 Mb) that harbors 15 genes. Furthermore, to identify additional loci for chicken growth, a genome‐wide association study (GWAS) was carried out in a WLA population. The GWAS identified an additional QTL on GGA6 for body weight at six weeks (19.8–21.2 Mb). Our findings showed that by using a WLA population we were able to further reduce the QTL confidence interval previously detected using a NHI × WL77 advanced intercross population.     

猪2号染色体遗传连锁图谱的构建与QTL定位分析

构建了猪2号染色体的遗传连锁图谱,并进一步进行了重要生产性状数量性状位点的定位,结果表明,7个微卫星位点均为中高度多态性位点,多态信息含量为0．40182－0．58477,可以满足遗传连锁图谱构建的要求,构建的资源家系遗传连锁图谱总长152．9cM,位点的排列顺序与USDA结果一致,但除了Sw2516与Sw1201标记区间外,所有标记区间距离均大于USDA图谱,将连锁图谱与性状记忆结合起来,进一步进行了猪数量性状位点定位的研究,在2号染色体发现了显著影响活体估测瘦肉率等活体估测性状的QTLs,此外还发现眼肌高度和背最长肌大理石纹的QTLs,其中影响活体估测瘦肉率的QTL达到了染色体显著的水平（P＜0．01）,且解释性状的表型变异达21．55％,影响眼肌高度和背最长肌大理石纹的QTLs分别可以解释10．12％和10．97％的表型变异,影响活体估测性状的QTLs加性效应与显性效应作用方向相反,影响眼肌高度的QTL加性效应与显性效应相同,在大白猪中具有增效等位基因,定位的QTLs效应较大,为在群体中开展分子标记辅助育种奠定了理论基础。     

Genetic dissection of the role of ethylene in regulating auxin-dependent lateral and adventitious root formation in tomato

In this study we investigated the role of ethylene in the formation of lateral and adventitious roots in tomato ( Solanum lycopersicum ) using mutants isolated for altered ethylene signaling and fruit ripening. Mutations that block ethylene responses and delay ripening – Nr ( Never ripe ), gr ( green ripe ), nor ( non ripening ), and rin ( ripening inhibitor ) – have enhanced lateral root formation. In contrast, the epi ( epinastic ) mutant, which has elevated ethylene and constitutive ethylene signaling in some tissues, or treatment with the ethylene precursor 1-aminocyclopropane carboxylic acid (ACC), reduces lateral root formation. Treatment with ACC inhibits the initiation and elongation of lateral roots, except in the Nr genotype. Root basipetal and acropetal indole-3-acetic acid (IAA) transport increase with ACC treatments or in the epi mutant, while in the Nr mutant there is less auxin transport than in the wild type and transport is insensitive to ACC. In contrast, the process of adventitious root formation shows the opposite response to ethylene, with ACC treatment and the epi mutation increasing adventitious root formation and the Nr mutation reducing the number of adventitious roots. In hypocotyls, ACC treatment negatively regulated IAA transport while the Nr mutant showed increased IAA transport in hypocotyls. Ethylene significantly reduces free IAA content in roots, but only subtly changes free IAA content in tomato hypocotyls. These results indicate a negative role for ethylene in lateral root formation and a positive role in adventitious root formation with modulation of auxin transport as a central point of ethylene–auxin crosstalk.     

Foraging environment determines the genetic architecture and evolutionary potential of trophic morphology in cichlid fishes

Phenotypic plasticity allows organisms to change their phenotype in response to shifts in the environment. While a central topic in current discussions of evolutionary potential, a comprehensive understanding of the genetic underpinnings of plasticity is lacking in systems undergoing adaptive diversification. Here, we investigate the genetic basis of phenotypic plasticity in a textbook adaptive radiation, Lake Malawi cichlid fishes. Specifically, we crossed two divergent species to generate an F₃ hybrid mapping population. At early juvenile stages, hybrid families were split and reared in alternate foraging environments that mimicked benthic/scraping or limnetic/sucking modes of feeding. These alternate treatments produced a variation in morphology that was broadly similar to the major axis of divergence among Malawi cichlids, providing support for the flexible stem theory of adaptive radiation. Next, we found that the genetic architecture of several morphological traits was highly sensitive to the environment. In particular, of 22 significant quantitative trait loci (QTL), only one was shared between the environments. In addition, we identified QTL acting across environments with alternate alleles being differentially sensitive to the environment. Thus, our data suggest that while plasticity is largely determined by loci specific to a given environment, it may also be influenced by loci operating across environments. Finally, our mapping data provide evidence for the evolution of plasticity via genetic assimilation at an important regulatory locus, ptch1. In all, our data address long‐standing discussions about the genetic basis and evolution of plasticity. They also underscore the importance of the environment in affecting developmental outcomes, genetic architectures, morphological diversity and evolutionary potential.     

Identification and characterisation of the tomato parthenocarpic mutant high fruit set under stress (hfs) exhibiting high productivity under heat and salt stress

Pollination and therefore fruit set in tomato (Solanum lycopersicum) is very sensitive to temperature. Parthenocarpy can be a very useful trait in tomato breeding in sustainable agriculture faced with global warming. Within a collection of Moneymaker tomato mutants a monogenic and recessive mutant with high fruit number was identified in heat stress conditions and named high fruit set under stress (hfs). No morphological alterations in vegetative and reproductive organs were observed except the bigger size of ovary. hfs is parthenocarpic, pollination not being required for fruit set, although this trait was not absolute since it produced some under‐seeded fruit. When plants were grown under extreme temperatures (higher than 35°C), hfs exhibits higher fruit yield than wild‐type (WT) due to increased fruit number. Another very interesting characteristic of hfs is its improved fruit quality under heat stress, exhibiting a better sweetness/acidity balance than WT. Interestingly, hfs was also tolerant to the combination of heat and salt stress, and the positive effect on production was due to both components of yield, fruit number and fruit weight. The generation of mostly seedless fruit and the high productivity and fruit quality under extreme temperatures make hfs a very interesting mutant to obtain new breeding high‐yield lines in adverse environmental conditions.     

Genetic dissection of bread wheat diversity and identification of adaptive loci in response to elevated tropospheric ozone

Rising tropospheric ozone affects the performance of important cereal crops thus threatening global food security. In this study, genetic variation of wheat regarding its physiological and yield responses to ozone was explored by exposing a diversity panel of 150 wheat genotypes to elevated ozone and control conditions throughout the growing season. Differential responses to ozone were observed for foliar symptom formation quantified as leaf bronzing score (LBS), vegetation indices and yield components. Vegetation indices representing the carotenoid to chlorophyll pigment ratio (such as Lic2) were particularly ozone-responsive and were thus considered suitable for the non-invasive diagnosing of ozone stress. Genetic variation in ozone-responsive traits was dissected by a genome-wide association study (GWAS). Significant marker-trait associations were identified for LBS on chromosome 5A and for vegetation indices (NDVI and Lic2) on chromosomes 6B and 6D. Analysis of linkage disequilibrium (LD) in these chromosomal regions revealed distinct LD blocks containing genes with a putative function in plant redox biology such as cytochrome P450 proteins and peroxidases. This study gives novel insight into the natural genetic variation in wheat ozone response, and lays the foundation for the molecular breeding of tolerant wheat varieties.     

Evolutionary and ecological functional genomics,from lab to the wild

Plant phenotypes are the result of both genetic and environmental forces that act to modulate trait expression. Over the last few years, numerous approaches in functional genomics and systems biology have led to a greater understanding of plant phenotypic variation and plant responses to the environment. These approaches, and the questions that they can address, have been loosely termed evolutionary and ecological functional genomics (EEFG), and have been providing key insights on how plants adapt and evolve. In particular, by bringing these studies from the laboratory to the field, EEFG studies allow us to gain greater knowledge of how plants function in their natural contexts.     

不同形态钙对高温逆境下番茄叶片光合作用的调控作

以‘辽园多丽’番茄幼苗为试材,在高温胁迫下喷施氯化钙(CaCl₂)、纳米钙(Nano-Ca)和糖醇钙(Manntiol-Ca),研究不同形态钙处理对高温逆境下番茄叶片光合作用的调控作用.结果表明: 不同形态的钙处理均可抑制高温逆境下叶片中叶绿素a和类胡萝卜素含量的下降;显著提高净光合速率(P_n),不同程度提高蒸腾速率(T_r)和气孔导度(g_s);降低PSII非调节性能量耗散的量子产量\[Y(NO)\]和由于受体侧限制引起的PSI非光化学能量耗散的量子产量\[Y(NA)\],提高PSII调节性能量耗散的量子产量\[Y(NPQ)\]和由于供体侧限制引起的PSI非光化学能量耗散的量子产量\[Y(ND)\];提高叶片中钙含量;Manntiol-Ca和Nano-Ca处理的总体效果优于CaCl₂处理.与CaCl₂相比,Manntiol-Ca和Nano-Ca是提高高温逆境下番茄叶片光合作用更有效的钙制剂.