QTLs and candidate genes for chlorate resistance in rice (Oryzasativa L.)

Chlorate resistance is one of the reliable characters in Indica/Japonica classification. To understand the genetic basis of chlorate resistance is very important for revealing the evolutionary mechanism of Indica/Japonica differentiation. In this study, a doubled haploid (DH) population derived from anther culture of ZYQ8/JX17, a typical Indica and Japonica hybrid, was used as the genetic material to investigate chlorate sensitivity of the parents and DH lines. The quantitative trait loci (QTLs) of chlorate resistance were analyzed based on the molecular linkage map of this population. Total of 3 QTLs (qCHR-2, qCHR-8 and qCHR-10) for chlorate resistance were detected on chromosomes 2, 8 and 10, respectively. A QTL × QTL epistatic interaction was detected between qCHR-2 and qCHR-10. Genes involved in nitrogen assimilation, such as nitrate reduction, molybdenum cofactor biosynthesis and nitrate transport were strong candidates of QTLs for chlorate resistance. A putative nitrate reductase gene (8611.t00011), and two putative nitrate reductase genes (9319.t00010 and 9319.t00012) were in the genomic region of qCHR-2, and qCHR-8, respectively, and a putative nitrate transporter gene (756.t00011) was in the region of qCHR-10. The expression of 8611.t00011, 9319.t00010 and 756.t00011 were confirmed by the corresponding cDNAs, and 2 in/del and 12 SNPs in the coding regions of these three genes were found between Indica (cv. 9311) and Japonica (cv. Nipponbare) in silico. These results indicated that these three genes were candidates of the chlorate resistance QTLs. An in/del in the coding region of 8611.t00011 was used to develop a new PCR marker. A polymorphism was detected between JX17/Nipponbare and ZYQ8/9311. This polymorphism corresponds to the chlorate sensitivity of Nipponbare and 9311. This marker was located between Y8007R and RM250 on chromosome 2 in the DH population, where qCHR-2 was also located.     

Quantitative trait loci (QTL) affecting sugars, organic acids and other biochemical properties possibly contributing to flavor, identified in four advanced backcross populations of tomato

Although the Advanced Backcross strategy has proven very useful for QTL detection in tomato, it has been used mainly in identifying QTL for agronomic traits such as yield, color, etc. Tomato flavor is an important quality characteristic, yet it has been difficult to assess flavor or traits that affect it. In this study the AB-QTL strategy was applied to four advanced backcross populations to identify QTL for biochemical properties that may contribute to the flavor of processed tomatoes, such as sugars and organic acids. A total of 222 QTL were identified for 15 traits, including flavor as assessed by a taste panel. Correlations of certain biochemicals with flavor and possible methods of assessing and improving flavor are discussed. In particular, QTL with very significant effects associated with the ratio of sugars/glutamic acid, a trait highly correlated with improved flavor, have been identified as good targets for future work in improving the flavor of tomatoes. This revised version was published online in August 2006 with corrections to the Cover Date.     

小麦7D染色体数量性状基因定位和效应估计的研究

综合应用方差分析法、区间定位法和联合定位法将控制抽穗期、有效穗数、小穗数、５０粒重和单穗产量等５个性状的６个数量性状基因座（ＱＴＬ）定位在小麦７Ｄ染色体上。其中控制粒重的ＱＴＬ有２个。这些ＱＴＬ集中分布在着丝粒附近和染色体长臂的末端两个区域。效应估计结果表明多数ＱＴＬ的效应是微效的，控制同一个性状（粒重）的两个ＱＴＬ的效应几乎相等。比较３种ＱＴＬ定位法的分析结果，方差分析简单有效，且当染色体上只有     

Mapping genes for grain protein concentration and grain yield on chromosome 5B of Triticum turgidum (L.) var. dicoccoides

Grain protein concentration (GPC) is an important quality factor in durum wheat [Triticum turgidum (L.) var. durum]. Due to the strong environmental influence on GPC, molecular markers linked to quantitative trait loci (QTL) affecting GPC have the potential to be valuable in wheat breeding programs. Various quantitative traits in a population of 133 recombinant inbred chromosome lines were studied in replicated trials at three locations in North Dakota. Segregation for GPC, 1000-kernel weight, gluten strength, heading date, and plant height was observed. By relating phenotypic data to a linkage map obtained from the same population, three QTL affecting GPC, and one affecting yield were identified. The genotypic coefficients of determination for both traits were high.     

栽培种花生遗传图谱的构建及主茎高和总分枝数QTL分析

栽培种花生是异源四倍体,基因组大,构建花生的分子遗传连锁图谱并对相关性状进行QTL定位研究的工作缓慢。本研究以遗传差异大的亲本组配杂交组合富川大花生×ICG6375构建F2作图群体,采用公开发表的2653对SSR引物,构建了一张含有234个SSR标记、分布于20个连锁群的栽培种花生遗传图谱。该图谱覆盖基因组的长度为1683.43c M,各个连锁群长度在36.11~131.48 c M之间,每个连锁群的标记数在6~15个之间,标记间的平均距离为7.19 c M。结合F3在湖北武汉和阳逻环境下的主茎高和总分枝数鉴定结果,应用Win QTLCart 2.5软件采用复合区间作图法进行了QTL定位和遗传效应分析。共检测到17个与主茎高和总分枝数相关的QTL位点,贡献率在0.10%~10.22%之间,分布于8个连锁群上。综合分析武汉和阳逻环境的鉴定结果,获得重复一致的与主茎高相关的6个QTL,其中q MHA061.1和q MHA062.1位于连锁群LG06上TC1A2~AHGS0153标记区间,贡献率为5.49%~8.95%;q MHA061.2和q MHA062.2位于LG06上AHGS1375~PM377标记区间,贡献率为2.93%~5.83%;q MHA092.2和q MHA091.1位于连锁群LG09上GM2839~EM87标记区间,贡献率为0.53%~9.43%。     

Prediction of heterosis using QTLs for yield traits in rapeseed (Brassica napus L.)

Three double low (erucic acid and glucosinolates) self-incompatible lines and 22 varieties from different origins were selected to produce 66 hybrids according to a NC II mating design. Field experiments for identification of hybrid performance and heterosis were conducted in two successive rapeseed growing seasons in Wuhan, China. After heterosis identifications, SI-1300 and Eagle were chosen to construct an F₂ segregating population. One hundred and eighty four F_2:3 lines were planted at Wuhan and Jingmen to test yield traits. F₂ plants and the 25 parents were analyzed using simultaneously AFLP (amplified fragment length polymorphism) and SSR (simple sequence repeat) markers. A total of 270 and 718 polymorphic loci were detected in the F₂ population and among the 25 parental lines, respectively. Of the 718 polymorphic loci, 178 were significantly correlated to yield traits. With the use of one-way ANOVA, 84 common QTLs were detected for 12 traits at two trial locations. Although the genetic distances based on general/specific heterozygosities and single-locus QTLs showed significant correlations with hybrid performance and heterosis for some yield traits, the determination coefficients were low. The results suggested that neither heterozygosities nor QTLs for yield traits were suitable to predict hybrid performance and heterosis in Brassica napus.     

Congruence of conventional and molecular studies to locate genes that control flavone synthesis in maize silks

The presence of maysin, a flavone glycoside, and its analogues in the silks of corn is an important defence against invasion of the ear by corn earworm in the southeastern USA. Three dent maize inbreds with high silk‐maysin concentrations were evaluated for chromosomal location of major genes controlling synthesis of three antibiotic chemicals by crossing them to a series of waxy‐marked chromosome 9 reciprocal translocations. The data indicated that genes for maysin and its analogues are probably present on the short arms of chromosomes 1 and 10, and long arms of chromosomes 5 and 8 for inbred line GT114, the short arms of chromosome 1 and 6, and the long arms of chromosome 5 and 8 for inbred line GE37, and the short arms of chromosomes 1 and 10, and the long arm of chromosome 4 for inbred line SC102. These results are in general agreement with other translocation studies on corn earworm injury to sweet corn inbreds and gene and restriction fragment length polymorphism marker studies to locate quantitative trait loci (QTL) for maysin synthesis, with the exception that QTL on chromosome 9 have been found to be strongly associated with flavone synthesis. The most significant concordance between conventional and molecular techniques for locating chromosome regions influencing synthesis of antibiotic chemicals from silks of high silk antibiosis sources is found for the short arm of chromosome 1. This region is the most likely one on which to place emphasis during the initial stages of transferring high‐maysin silks to elite inbred lines. A chromosome 1 marker plus at least one more from any chosen high‐maysin inbred source should be sufficient to transfer high maysin silks to other lines. Other markers may be needed for transfer of specific traits when recovering recurrent parent genome types in a backcrossing procedure.     

QTL analysis of seed dormancy in rice (Oryza sativa L.)

Effective cumulative temperature (ECT) after heading would be a more reasonable parameter for seed sampling of pre-harvest sprouting/seed dormancy (SD) tests in segregating populations than the days after flowering. SD is an important agronomic trait associated with grain yielding, eating quality and seed quality. To identify genomic regions affecting SD at different grain-filling temperatures, and to further examine the association between SD and ECT during grain-filling, 127 double haploid (DH) lines derived from a cross between ZYQ8 (indica)/JX17 (japonica) by anther culture were analyzed. The quantitative trait loci (QTLs) and their digenic epistasis for SD were identified using a molecular linkage map of this population. A total of four putative QTLs for SD (qSD-3, qSD-5, 6 and 11) were detected on chromosomes 3, 5, 6 and 11, together explaining 41.4% of the phenotypic variation. Nine pairs of digenic epistatic loci were associated with SD on all but chromosome 9, and their contributions to phenotypic variation varied from 2.87%–8.73%. The SD QTL on chromosome 3 was identical to the QTLs found in other mapping populations with different genetic backgrounds, which could be a desirable candidate for gene cloning and marker-assisted selection in rice breeding.     

Mapping QTL involved in adult plant resistance to powdery mildew in the winter wheat line RE714 in two susceptible genetic backgrounds

The objective was to study the genetic basis of adult plant resistance to powdery mildew of the winter wheat line RE714 by quantitative trait loci (QTL) analysis and to investigate the stability of the QTL detected in two different genetic backgrounds. Two DH populations from the crosses between RE714 and the susceptible parents ‘Festin’ and ‘Hardi’ were used. Reaction of the DH lines to powdery mildew was assessed in different environments in Belgium under natural disease infection. Considering both populations and according to the environment tested, one to seven QTL were detected. Among them, residual effects of the race‐specific resistance genes Pm4b and MIRE were found. Two major QTL were very stable (on chromosome 5D and at the MIRE locus), since they were detected in both populations and over all environments tested. The QTL detected varied according to the susceptible parent used, and a residual effect at the Pm4b gene was not observed with the genetic background of ‘Hardi’.     

Mapping genes for deep-seeding tolerance in barley

Deep-seeding tolerance, the emergence of seedlings from deep seeded conditions, is involved in stand establishment in semi-arid regions, where the soil surface is too dry for seed germination. Genes determining deep-seeding tolerance in barley were mapped using two doubled haploid populations derived from the following crosses: Harrington × TR306 (H/T)and Step toe × Morex (S/M). Significant quantitative trait loci (QTLs) for deep-seeding tolerance were found in each population. Two QTL sex plained 40% of the phenotypic variation in the H/T population and one QTL (S/M) 8% of the total phenotypic variance. Multiple QTLs accounting for coleoptile length and first internode length were detected in both populations. In the H/T population, there were coincident QTLs for deep-seeding tolerance, coleoptile length and first internode length on the long arm of chromosome 5H. These QTLs correspond with previously reported QTLs for abscisic acid and gibberellic acid response. QTL coincidence may be due to the pleiotropic effects of alleles at a single locus. This information may be useful for breeding programs manipulating morphological and physiological traits in order to develop varieties for semi-arid regions. This revised version was published online in August 2006 with corrections to the Cover Date.