Identification of Quantitative Trait Loci (QTLs) for Fruit Quality Traits in Apple

A segregating mapping population of “Co-op 17” × “Co-op 16” was used to identify quantitative trait loci (QTLs) associated with various fruit quality traits in apple. Phenotypic data were collected over 2 years for fruit circumference (in centimeter), diameter at midpoint (in centimeter), length (in centimeter), weight (in gram), total soluble solids (in degree Brix), and total titratable acids (in percent) for the segregating population. The phenotypic data along with a previously constructed genetic map, based on simple sequence repeat markers derived from expressed sequence tag and bacterial artificial chromosome end sequence databases, were used in marker–trait association analysis. Interval mapping identified two QTLs linked to fruit size components on linkage groups 03 and 05 with limit of detection scores of 3.27–4.06 and 3.29–4.02 along with phenotypic variation accounting for 15.4–46.4 and 18.3–21.9 %, respectively.     

小麦旗叶长、宽及面积的QTL分析

以小麦品种‘小偃81’和‘西农1376’构建的含236个家系的自交重组系(RIL)群体(F2:7、F2:8代)为研究材料,采用完全随机区组设计,连续2年在陕西杨陵、河南驻马店和山东济南于灌浆期(花后20d)随机取每个株系10株测量旗叶长、宽,并利用172个SSR标记构建了遗传连锁图谱,通过基于完备区间作图法的QTL IciMapping V3.2软件,对控制小麦旗叶长、宽和面积的数量性状位点(QTL)进行了加性效应分析。结果发现:(1)9个旗叶长QTLs位于1A、4A、3B、5D和7D染色体上,单个QTL可解释5.10%~16.44%的表型变异;10个旗叶宽QTLs位于1A、3A、5A、7A、3B和5D染色体上,单个QTL可解释4.63%~14.24%的表型变异;12个旗叶面积QTLs位于1A、4A、3B、2D和5D染色体上,单个QTL可解释4.25%~22.67%的表型变异。(2)控制小麦旗叶长、宽和面积的QTLs存在差异,同一QTL在不同性状中的遗传贡献率也不同。(3)同一性状在同一年份,不同地点和在不同年份,相同地点下检测到的QTLs有的相同,但有的差异明显。(4)有些控制不同性状的QTLs在染色体的同一标记区间,表现一因多效。研究表明:位于1A和5D染色体上的2个加性QTLs都同时控制旗叶长、宽和面积,且前者为主效基因,后者遗传贡献率也较大,可用于标记辅助育种和分子聚合育种。     

Transmission of Fruit Quality Traits in Apricot (Prunus armeniaca L.) and Analysis of Linked Quantitative Trait Loci (QTLs) Using Simple Sequence Repeat (SSR) Markers

Twelve important pomological traits related to fruit quality were studied during 3 years in an F₁ apricot progeny of 160 seedlings derived from a cross between the Spanish selection ‘Z701-1’ and the South African cultivar ‘Palsteyn’. Results indicated quantitative transmission of most of the fruit quality traits studied. In addition, a clear influence of the genetic background of parents was observed. In some seedlings, values outside the range of the parent were observed due to the influence of this genetic background. No correlations were found among most agronomic traits in apricot during the 3 years of the study. However, high correlations between years were described for most of the evaluated traits, and the environment had limited influence on the expression of the trait. A genetic map was developed using 41 apricot and peach SSR markers. The map obtained showed eight linkage groups (corresponding to the eight chromosomes) covering a total distance of 369.3 cM and an average distance between markers of 9 cM. Fifty-four QTLs associated with different traits were identified, including: blooming date (linkage groups G1, G4 and G7); ripening time (G4 and G6); fruit development (G4 and G6); fruit weight (G1 and G4); stone weight (G1 and G7); flesh color (G1 and G6); pH (G1, G2 and G4); malic acid (G1, G2 and G4); and soluble solids content (G4 and G5). We have highlighted several QTLs in G4 that explain the variability in various traits related to fruit quality such as blooming date, ripening time, and soluble solids content. In addition, we have also highlighted an important QTL on G2 that explains much of the variation in levels of acidity.     

Relationship Between Abscisic Acid and Apricot Fruit Ripening

Changes in levels of growth regulating substances during fruit development and maturation and the effects of abscisic acid application on ripening of apricot fruits were investigated. The results showed that the levels of growth promoting substances were high, but started to decrease rapidly just before the end of stage Ⅱ and continued throughout stage Ⅲ. The promoting substances almost disappeared in fully ripe fruits. The ABA-like inhibiting substances first appeared during the end of stage Ⅱ, increased significantly in stage Ⅲ, and reached a maximum level in fully ripe fruits. Exogenous ABA application enhanced fruit respiration rate and accelerated the ripening process when applied to preclimacteric fruits but inhibited these processes when applied to post-climacteric fruits. The above results suggested that the ABA may play an important role in apricot fruit ripening. The interrelationship of ABA, ethylene, and fruit ripening was discussed.     

Mapping and characterization of novel parthenocarpy QTLs in tomato

Parthenocarpy is the development of the fruit in absence of pollination and/or fertilization. In tomato, parthenocarpy is considered as an attractive trait to solve the problems of fruit setting under unfavorable conditions. We studied the genetics of parthenocarpy in two different lines, IL5-1 and IVT-line 1, both carrying Solanum habrochaites chromosome segments. Parthenocarpy in IL5-1 is under the control of two QTLs, one on chromosome 4 (pat4.1) and one on chromosome 5 (pat5.1). IVT-line 1 also contains two parthenocarpy QTLs, one on chromosome 4 (pat4.2) and one on chromosome 9 (pat9.1). In addition, we identified one stigma exsertion locus in IL5-1, located on the long arm of chromosome 5 (se5.1). It is likely that pat4.1, from IL5-1 and pat4.2, from IVT-line 1, both located near the centromere of chromosome 4 are allelic. By making use of the microsynteny between tomato and Arabidopsis in this genetic region, we identified ARF8 as a potential candidate gene for these two QTLs. ARF8 is known to act as an inhibitor for further carpel development in Arabidopsis, in absence of pollination/fertilization. Expression of an aberrant form of the Arabidopsis ARF8 gene, in tomato, has been found to cause parthenocarpy. This candidate gene approach may lead to the first isolation of a parthenocarpy gene in tomato and will allow further use in several crop species.     

Mapping QTLs for alpha-amylase activity in rye grain

Genetic control of alpha-amylase activity in rye grain was investigated by QTL mapping based on DS2 x RXL10 intercross consisting of 99 F5-6 families propagated at one location during four vegetation seasons. A wide range of variation in alpha-amylase activity and transgression effects were found among families and parental lines. This variation was shown to be determined in 40.1% by 7 significant (LOD score not less than 2.5) and 2 putative QTLs (2 < LOD < 2.5) distributed on all rye chromosomes except 4R. Two significant QTLs located on 3RL and 5RL chromosome arms were expressed each year. The third significant QTL was detected in three years (1RL). The other four significant QTLs (2RL, 5RS, 6RL, 7RL) were found in one year of study. The number and composition of QTLs were specific for a given year varying from three to six. QTLs were not correlated with isoenzyme polymorphisms at the structural alpha-Amy1 loci. A QTL associated with a region containing the alpha-Amy3 locus was detected on chromosome 5RL. Both high- and low-activity QTL alleles were found in each parental line, which explains the appearance of transgressive recombinants in the segregating population.     

水稻叶绿素含量的QTL定位

利用由两个籼稻品种Acc8558和H359杂交构建的一个包含131个株系(F19)的重组自交系群体,及其相应的包含147个RFLP和78个AFLP标记的遗传图谱,采用多性状复合区间定位方法,对控制水稻叶绿素含量的QTL进行了定位分析。对叶绿素a和叶绿素b含量各检测到6个QTL,其中5个QTL在两性状问是相同的。这些QTL主要分布在第1和第4染色体上,因此这两条染色体对叶绿素含量是重要的。QTL qChlAlc／qChlBlb(二者位置相同)在4个观测时期均表现较大效应,且在最后的剑叶期贡献最大,因此对叶绿素含量最为重要。另两个QTL(qCh-LA4a／qChlB4a和qChlA4b／qChlB4b)只在第2次观测时期效应显著,表明它们只在特定发育阶段发挥作用。     

Mapping of QTLs governing agronomic and yield traits in chickpea

Chickpea is one of the most important leguminous cool season food crops, cultivated prevalently in South Asia and Middle East. The main objective of this study was to identify quantitative trait loci (QTLs) associated with seven agronomic and yield traits in two recombinant inbred line populations of chickpea derived from the crosses JG62 × Vijay (JV population) and Vijay × ICC4958 (VI population) from at least three environments. Single locus QTL analysis involved composite interval mapping (CIM) for individual traits and multiple-trait composite interval mapping (MCIM) for correlated traits to detect pleiotropic QTLs. Two-locus analysis was conducted to identify the main effect QTLs (M-QTLs), epistatic QTLs (E-QTLs) and QTL × environment interactions. Through CIM analysis, a total of 106 significant QTLs (41 in JV and 65 in VI populations) were identified for the seven traits, of which one QTL each for plant height and days to maturity was common in both the populations. Six pleiotropic QTLs that were consistent over the environments were also identified. LG2 in JV and LG1a in VI contained at least one QTL for each trait. Hence, concentrating on these LGs in molecular breeding programs is most likely to bring simultaneous improvement in these traits.     

甘蓝分子连锁图的构建与品质性状的QTL定位

以两个不同生态型甘蓝(Brassica oleracea var．capitata)品种杂交得到的F2代为作图群体,用RAPD标记构建甘蓝分子连锁图。通过对520个随机引物进行筛选,236个引物在两亲本间表现多态性,多态性比例为47．7％。选取111个引物对群体进行分析,构建了一张含有135个标记位点,9个连锁群,覆盖长度为1023．7cM的分子连锁图。利用该图谱对甘蓝叶球紧实度和中心柱长两性状进行了QTL定位分析。检测到3个与叶球紧实度相关的QTL,总贡献率为62．5％;检测到4个与中心柱长相关的QTL,总贡献率为59．1％。     

Mapping QTLs associated with drought resistance in rice: Progress, problems and prospects

The use of molecular markers in the mapping of traits of agronomic importance holds great promise for speeding the development of improved plant varieties and increasing our understanding of the physiological or molecular mechanisms behind biological phenomena. The technique is now being applied to drought resistance in rice (Oryza sativa L.). Drought is important because a considerable proportion of the world rice area is not irrigated and can be prone to water deficit. A large number of people, particular some of the poorest rice farmers, stand to gain if new varieties which combine high yield and drought resistance can be developed. Rice should be particularly useful for the molecular genetic analysis of drought resistance because of its growing role as a model monocot species and the diversity of drought resistance mechanisms which are found in the germplasm. We briefly review the traits which might be considered important in improving drought resistance in rice, before explaining the molecular mapping approach. We review progress at locating quantitative trait loci (QTLs) for individual mechanisms of drought resistance in controlled environment conditions. This includes a detailed comparison of reported QTLs related to root morphological characters. The search for QTLs associated with field performance under drought stress is analysed and the problems associated with understanding the genetic control of a complex physical and physiological phenomenon under conditions of substantial environmental variation are highlighted. We emphasise that the use of near isogenic lines in overcoming some of the problems offers considerable promise for the future.(seconded from CIRAD-CA, France)     

Mapping of FHB resistance QTLs in tetraploid wheat.

Triticum turgidum L var. durum is known to be particularly susceptible to infection by Fusarium graminearum, the causal agent for Fusarium head blight (FHB), which results in severe yield losses and grain contaminated with mycotoxins. This research was aimed at identifying FHB resistance in tetraploid wheat and mapping the location of FHB resistance genes. A tetraploid cross of durum wheat ('Strongfield') x Triticum carthlicum ('Blackbird') was used to generate a doubled-haploid (DH) population. This population was evaluated for type II resistance to F. graminearum in replicated greenhouse trials, in which heads were innoculated and the percent of infected spikelets was determined 21 days later. The population was also genotyped with microsatellite markers to construct a map of 424 loci, covering 2 052 cM. The FHB reaction and genotypic data were used to identify FHB resistance quantitative trait loci (QTLs). It was determined that 2 intervals on chromosomes 2BL and 6BS controlled FHB resistance in this tetraploid cross. The FHB resistance allele on chromosome 2BL (r2=0.26, logarithm of odds (LOD)=8.5) was derived from 'Strongfield', and the FHB resistance allele on chromosome 6BS (r2=0.23, LOD=6.6) was derived from 'Blackbird'. Two other loci, on chromosomes 5AS and 2AL, were shown to regulate FHB infection and to have an epistatic effect on the FHB resistance QTL on chromosome 6BS. Further, the FHB resistance QTL peak on chromosome 6BS was clearly coincident with the known FHB resistance gene Fhb2, derived from Sumai 3. The results show that FHB resistance can be expressed in durum wheat, and that T. carthlicum and Triticum aestivum likely share a common FHB resistance gene on chromosome 6BS.     

Mapping QTLs associated with drought avoidance in upland rice

The identification of molecular markers linked to genes controlling drought resistance factors in rice is a necessary step to improve breeding efficiency for this complex trait. QTLs controlling drought avoidance mechanisms were analyzed in a doubled-haploid population of rice. Three trials with different drought stress intensities were carried out in two sites. Leaf rolling, leaf drying, relative water content of leaves and relative growth rate under water stress were measured on 105 doubled haploid lines in two trials and on a sub-sample of 85 lines in the third one. Using composite interval mapping with a LOD threshold of 2.5, the total number of QTLs detected in all trials combined was 11 for leaf rolling, 10 for leaf drying, 11 for relative water content and 10 for relative growth rate under stress. Some of these QTLs were common across traits. Among the eleven possible QTLs for leaf rolling, three QTLs (on chromosomes 1, 5 and 9) were common across the three trials and four additional QTLs (on chromosomes 3, 4 and 9) were common across two trials. One QTL on chromosome 4 for leaf drying and one QTL on chromosome 1 for relative water content were common across two trials while no common QTL was identified for relative growth rate under stress. Some of the QTLs detected for leaf rolling, leaf drying and relative water content mapped in the same places as QTLs controlling root morphology, which were identified in a previous study involving the same population. Some QTL identified here were also located similarly with other QTLs for leaf rolling as reported from other populations. This study may help to chose the best segments for introgression into rice varieties and improvement of their drought resistance.     

应用频数分布面积法定位家蚕QTL

利用生态型差异较大的两个家蚕品种７８２和ｏｄ１００作正反杂交,得到Ｆ１。让Ｆ１雄蚕与叠双隐性标记的ｏｄ１００回 到回交子代。     

Evaluation of Some Phenological and Biochemical Characteristics of Selected New Late Flowering Dried Apricot Cultivars

In this study, promising candidates of six apricot genotypes were compared with our local and major cultivar (Hac?halilo?lu) based on their phenological, pomological, and biochemical characteristics. Fruit weight, stone weight, flesh firmness, flesh fruit/stone ratio, TSS (Total soluble solids), glucose, fructose, sucrose, total phenols, total antioxidant activity (FRAP and ABTS assays) and bud break, first bloom, full bloom, and harvesting date of apricot cultivar candidates were compared with cultivar Hac?halilo?lu ‘HH.’ According to the obtained results, the higher content of total phenolic compounds and total antioxidant activity was determined in the N95 genotype (96.87 µmol TE/g) fruit, whereas the ‘HH’ cultivar was characterized by the lower value (94.6 µmol TE/g) especially determined by FRAP method. Individual sugars and the soluble solids content of fruit differed between selected genotypes and ‘HH’ cultivar. Glucose, fructose, and sucrose contents were higher in all selected genotypes than in Hac?halilo?lu cultivar.     

Mapping candidate QTLs related to plant persistency in red clover

Red clover (Trifolium pratense L.) is a diploid (2n = 14), self-incompatible legume that is widely cultivated as a forage legume in cold geographical regions. Because it is a short-lived perennial species, improvement of plant persistency is the most important objective for red clover breeding. To develop a marker-assisted selection (MAS) approach for red clover, we identified candidate QTLs related to plant persistency. Two full-sib mapping populations, 272 × WF1680 and HR × R130, were used for QTL identification. Resistance to Sclerotinia trifoliorum and Fusarium species, as well as to winter hardiness, was investigated in the laboratory and in field experiments in Moscow region (Russia), and Sapporo (Japan). With the genotype data derived from microsatellite and other DNA markers, candidate QTLs were identified by simple interval mapping (SIM), Kruskal–Wallis analysis (KW analysis) and genotype matrix mapping (GMM). A total of 10 and 23 candidate QTL regions for plant persistency were identified in the 272 × WF1680 and the HR × R130 mapping populations, respectively. The QTLs identified by multiple mapping approaches were mapped on linkage group (LG) 3 and LG6. The significant QTL interactions identified by GMM explained the higher phenotypic variation than single effect QTLs. Identification of haplotypes having positive effect QTLs in each parent were first demonstrated in this study for pseudo-testcross mapping populations in plant species using experimental data.     

Association Mapping for Fruit,Plant and Leaf Morphology Traits in Eggplant

An eggplant (Solanum melongena) association panel of 191 accessions, comprising a mixture of breeding lines, old varieties and landrace selections was SNP genotyped and phenotyped for key breeding fruit and plant traits at two locations over two seasons. A genome-wide association (GWA) analysis was performed using the mixed linear model, which takes into account both a kinship matrix and the sub-population membership of the accessions. Overall, 194 phenotype/genotype associations were uncovered, relating to 30 of the 33 measured traits. These associations involved 79 SNP loci mapping to 39 distinct chromosomal regions distributed over all 12 eggplant chromosomes. A comparison of the map positions of these SNPs with those of loci derived from conventional linkage mapping showed that GWA analysis both validated many of the known controlling loci and detected a large number of new marker/trait associations. Exploiting established syntenic relationships between eggplant chromosomes and those of tomato and pepper recognized orthologous regions in ten eggplant chromosomes harbouring genes influencing breeders’ traits.     

小麦幼苗耐热性的QTL定位分析

以小麦DH群体(‘旱选10号’ב鲁麦14’)为材料,在高温(热胁迫)及常温(对照)两种条件下考察小麦幼苗的根干重、苗干重、幼苗生物量、叶片叶绿素含量、叶绿素荧光参数及其耐热指数,并应用基于混合线性模型的复合区间作图法分析幼苗性状及其耐热指数QTL的数量、染色体分布及表达情况,以及QTL与环境的互作效应。结果显示:(1)亲本‘旱选10号’的耐热性明显优于‘鲁麦14’,且杂交后代的耐热性出现超亲分离。(2)控制幼苗耐热相关性状的QTL位点在染色体2D、6B、3A、4A、5A和7A上分布较多,而控制幼苗性状耐热指数的QTL在染色体6A、6B、3A、2D、5A和7A上分布较多,QTL位点在染色体上的分布有区域化的趋势。(3)控制幼苗性状的单个加性QTL和上位性QTL解释的表型变异分别平均为2.48%和2.65%;而控制耐热指数的单个加性QTL和上位性QTL解释的表型变异分别平均为8.84%和1.98%。(4)在热胁迫和对照条件下共检测到与幼苗性状及其耐热指数有关的加性效应QTL 13个和上位性效应QTL 28对,分布在除4D和6D以外的19条染色体上。研究表明,控制幼苗性状的QTL以上位性效应为主,而其耐热指数的QTL以加性效应为主。     

Mapping of QTLs involved in nematode resistance, tuber yield and root development in Solanum sp.

A backcross population, derived from the cross (S. tuberosumxS. spegazzinii)xS. tuberosum was used to map QTLs involved in nematode resistance, tuber yield and root development. Complete linkage maps were available for the interspecific hybrid parent as well as the S. tuberosum parent, and interval mapping for all traits was performed for both. Additionally, the intra- and inter-locus interactions of the QTLs were examined. The Gro1.2 locus, involved in resistance to G. rostochiensis pathotype Ro1, that was previously mapped in the S. tuberosumxS. spegazzinii F₁ population, was located more precisely on chromosome 10. A new resistance locus, Gro1.4, also conferring resistance to G. rostochiensis pathotype Ro1, was found on chromosome 3. Different alleles of this locus originating from both parents contributed to the resistant phenotype, indicating multiallelism at this locus. No interlocus interactions were observed between these two resistance loci. For resistance to G. pallida no QTLs were detected. One minor QTL involved in tuber yield was located on chromosome 4. Two QTLs involved in root development and having large effects were mapped on chromosomes 2 and 6 and an epistatic interaction was found between these two loci.