Genetic mapping within the wheat D genome reveals QTL for germination, seed vigour and longevity, and early seedling growth

Quantitative trait loci (QTL) controlling germination, seed vigour and longevity, and early seedling growth were identified using a set of common wheat lines carrying known D genome introgression segments. Seed germination (capacity, timing, rate and synchronicity) was characterized by a standard germination test, based either on the 1 mm root protrusion (germination sensu stricto) or the development of normal seedlings. To quantify seed vigour, the same traits were measured from batches of seed exposed for 72 h at 43°C and high (ca. 100%) humidity. Seed longevity was evaluated from the relative trait values. Seedling growth was assessed both under non-stressed and under osmotic stress conditions. Twenty QTL were mapped to chromosomes 1D, 2D, 4D, 5D, and 7D. Most of the QTL for germination sensu stricto clustered on chromosome 1DS in the region Xgwm1291–Xgwm337. A region on chromosome 7DS associated with Xgwm1002 harboured loci controlling the development of normal seedlings. Seed vigour-related QTL were present in a region of chromosome 5DL linked to Xgwm960. QTL for seed longevity were coincident with those for germination or seed vigour on chromosomes 1D or 5D. QTL for seedling growth were identified on chromosomes 4D and 5D. A candidate homologues search suggested the putative functions of the genes within the respective regions. These results offer perspectives for the selection of favourable alleles to improve certain vigour traits in wheat, although the negative effects of the same chromosome regions on other traits may limit their practical use.     

QTL for rice grain quality based on a DH population derived from parents with similar apparent amylose content

A doubled haploid (DH)population consisting of 135 lines, derived from an indica (IR64) and a japonica (Azucena) rice with a similar apparent amylose content (AAC), was used to investigate the genetic factors affecting cooking and eating quality of rice. AAC,gelatinization temperature (GT), gel consistency (GC) and six starch pasting viscosity parameters were measured for quantitative trait loci (QTL) analysis using 193 molecular markers mapped on the DH population. A total of 17 QTLs were detected for the 9 traits, with at least one QTL and as many as 3 QTLs for each individual trait. No QTL for the measured parameters was found at the wx locus,possibly because of the similar AAC between the parents. Several QTLs with important effects on the variations in the measured parameters were detected in the present study which have not been found in earlier reports based on populations derived from parents with different AAC and wxgene alleles. Two interesting loci could be deduced from the present study according to the marker order compared with other genetic linkage maps. A QTL flanked by Amy2A and RG433 on the end of the long arm of chromosome 6, identified for GT, set back and consistency viscosity, might cover the gene encoding starch branching enzyme I. Similarly, a QTL flanked by RG139 and RZ58on chromosome 2, detected for hot paste viscosity and breakdown viscosity, might cover the gene encoding starch branching enzyme III. Generally, traits significantly correlated with each other shared identical QTL, but it was not true in some cases. The fine molecular mechanisms underlying these traits await further elucidation for the improvement of eating and cooking quality of rice. This revised version was published online in August 2006 with corrections to the Cover Date.     

Molecular mapping of QTLs for domestication-related traits in cowpea (V. unguiculata (L.) Walp.)

Understanding the genetic basis underlying domestication-related traits (DRTs) of cowpea (Vigna unguiculata (L.) Walp.) is important since the genome has experienced divergent domestication and in addition it is also useful to utilize the wild germplasm efficiently for improving different traits of the cultivated cowpea. Quantitative trait loci (QTLs) for DRTs were identified in a population of 159 F₇ recombinant inbred lines derived from a cross between a domesticated cowpea (V. unguiculata (L.) Walp.) variety, 524B, and a wild accession, 219. Using the constructed linkage map, QTLs for 10 DRTs were analysed and mapped. QTLs for seed, pod and flower related traits were detected. Subsequently, QTL for ovule number was also identified. To our knowledge, this is the first time a QTL for this trait has been observed. QTLs for DRTs show co-localization on three linkage groups and pleiotropy or close linkage of genes for the traits is suggested in these chromosome regions. The information gained in this study can be used for marker-assisted selection of domestication-related QTLs in cowpea and enhance understanding of domestication in the genus Vigna.     

Construction of a genetic linkage map and QTL analysis of fiber-related traits in upland cotton (Gossypium hirsutum L.)

A genetic linkage map with 70 loci (55 SSR, 12 AFLP and 3 morphological loci) was constructed using 117 F₂ plants obtained from a cross between two upland cotton cultivars Yumian 1 and T586, which have relatively high levels of DNA marker polymorphism and differ remarkably in fiber-related traits. The linkage map comprised of 20 linkage groups, covering 525 cM with an average distance of 7.5 cM between two markers, or approximately 11.8% of the recombination length of the cotton genome. The present genetic linkage map was used to identify and map the quantitative trait loci (QTLs) affecting lint percentage and fiber quality traits in 117 F_2:3 family lines. Sixteen QTLs for lint percentage and fiber quality traits were identified in six linkage groups by multiple interval mapping: four QTLs for lint percentage, two QTLs for fiber 2.5% span length, three QTLs for fiber length uniformity, three QTLs for fiber strength, two QTLs for fiber elongation and two QTLs for micronaire reading. The QTL controlling fiber-related traits were mainly additive, and meanwhile including dominant and overdominant. Several QTLs affecting different fiber-related traits were detected within the same chromosome region, suggesting that genes controlling fiber traits may be linked or the result of pleiotropy.     

Construction of a genetic linkage map with SSR,AFLP and morphological markers to locate QTLs controlling pathotype-specific powdery mildew resistance in diploid roses

Disease resistance is a sought-after trait in plant breeding programmes. One strategy to make resistance more durable is to increase the number of resistance genes, thereby increasing the number of pathotypes withstood. One of the most important diseases on roses is powdery mildew (PM) (Podosphaera pannosa). Recent studies show that pathotypes of PM and different types of resistances in roses exist. The results of this study aim to contribute to PM resistance in roses by the development of pathotype-specific markers on a genetic map. A diploid rose population (90 genotypes) derived from a cross between Rosa wichurana and Rosa ‘Yesterday’ was used to construct a genetic linkage map encompassing 20 AFLP primer combinations, 43 SSR, and 2 morphological markers. By applying the F1 pseudo test cross population strategy, two parental linkage maps were constructed (parent ‘Yesterday’ 536 cM; parent R. wichurana 526 cM). Both parental maps consisted of seven linkage groups with an average length of 70 cM (Kosambi) corresponding to the seven haploid rose chromosomes. These new maps were used to identify QTLs controlling disease resistance. The offspring population was screened for resistance to two PM pathotypes, R–E and R–P. QTLs for controlling pathotype-specific disease resistance were mapped by applying Kruskal–Wallis rank-sum tests and simple interval mapping. With two pathotypes analysed, nine QTL loci were detected on linkage groups 2, 3, 5 and 6, explaining 15–73% of the phenotypic variance for pathotype-specific disease response. The genetic maps developed here will be useful for future rose breeding, pathotype-specific resistance research and development of a consensus map for roses.     

Quantitative trait locus mapping of floral and related traits using an F2 population of Aquilegia

The objective of this study was to determine quantitative trait loci (QTL) underlying ten floral and related traits in Aquilegia. The traits assessed were calyx diameter, corolla diameter, petal length, petal blade length, sepal length, sepal width, spur length, spur width, plant height and flower number. These are important traits for ornamental value and reproductive isolation of Aquilegia. QTL analysis of these traits was conducted using single‐marker analysis and composite interval mapping (CIM). We used an F₂ population consisting of 148 individuals derived from a cross between the Chinese wild species Aquilegia oxysepala and the cultivar Aquilegia flabellata ‘pumila’. Resulting CIM analysis identified 39 QTLs associated with these traits, which were mapped on seven linkage groups. These QTLs could explain 1.22–53.28% of the phenotypic variance. Thirty‐one QTLs, which explained more than 10% of the phenotypic variation, were classified as major QTLs. Graphical representations of the QTLs on seven linkage groups were made. Our research provides the potential for future molecular assisted selection breeding programmes and the cloning of target genes through fine mapping.     

Detection of quantitative trait locus for leaffolder (Cnaphalocrocis medinalis (Guenée)) resistance in rice on linkage group 1 based on damage score and flag leaf width

Rice leaffolder (RLF) (Cnaphalocrocis medinalis (Guenée) is a destructive and widespread insect pest throughout the rice growing regions in Asia. The genetics of resistance to RLF in rice is very complex and not thoroughly explored. The present study was conducted to detect the quantitative trait loci (QTL) associated with RLF resistance involving 176 recombinant inbred lines (RILs) of F₈ generation derived from a cross between IR36, a leaffolder susceptible variety and TNAULFR831311, a moderately resistant indica rice culture. Simple sequence repeat (SSR) markers were used to construct specific linkage groups of rice. All the RILs were screened to assess their level of resistance to RLF by measuring the leaf area damaged. Besides this, the length and width of the flag leaf of each RIL were measured since these two parameters were considered as correlated traits to the RLF resistance in rice. All the above parameters observed across the RILs showed quantitative variation. Correlation analysis revealed that damage score based on greenhouse screening was positively correlated with length and width of the flag leaf. Out of 364 SSR markers analysed, 90 were polymorphic between the parents. Multi-point analysis carried out on segregating 69 SSR marker loci linkage group wise resulted in construction of linkage map with eleven groups of 42 SSR markers. Through single marker analysis, 19 SSR markers were found to have putative association with the three phenotypic traits studied. Of these markers, RM472 was identified as a locus having major effect on RLF resistance trait based on length of the flag leaf. Interval mapping detected two QTLs on linkage group 1. Among these QTLs, the QTL flanked by RM576–RM3412 were found to be associated with width of the flag leaf and RLF resistance. The putative SSR markers associated with leaffolder resistance identified in the present study may be one of the loci contributing resistance to RLF in rice.     

用闭合三角形杂交群体检测QTL等位位点差异

本文简述QTL定位和数量性状分子标记辅助选择的基本原理、基本方法,以及在实际应用中存在的一些问题。将12个不同作图群体构建的刚UP或SSR分子标记连锁图,根据其大多数分子标记所在的染色体节,再按每条染色体在各自连锁图中的相对长度整合在一起,然后将所定位的玉米株高QTL转换成整合图上的相对位置。结果发现,12个作图群体定位的75个玉米株高QTL位点遍布整个染色体组,QTL定位的重演性不高。分析认为,这是数量性状受众多微效多基因控制的必然现象。最后,提出用闭合三角形杂交群体进行QTL定位,检测QTL等位点的多重差异,并设想用这种方法验证或提高不同作图群体定位同一数量性状QTL的重演性。     

陆地棉种子物理性状QTL定位

定位棉花种子性状的基因对揭示棉花种子性状的遗传规律,以及明确棉花种子、产量、纤维品质等性状间的遗传关系具有重要意义。以(渝棉1号×T586) F_2:7重组近交系群体构建的遗传连锁图谱,在鉴定270个家系3个环境种子物理性状的基础上,利用MQM作图方法,共检测到34个种子物理性状QTL,包括9个种子重(qSW)、5个短绒重(qFW)、3个短绒率(qFP)、8个种仁重(qKW)、6个种子壳重(qHW)和3个种仁率(qKP)QTL,它们可解释4.6%~80.1%的性状表型变异。9个QTL在2个或3个环境中被检测到,其中包括第12染色体显性光子位点的短绒重与短绒率QTL,以及另外7个微效应QTL。34个QTL分布于15条染色体,其中A染色体组20个,D染色体组14个。有12个染色体区段分布有2个或2个以上的QTL,而且同一染色体区域同一亲本所具有的不同性状QTL的方向大多数与性状表型相关系数的正负一致。     

QTL mapping of the domestication traits pre-harvest sprouting and dormancy in wheat (<Emphasis Type="BoldItalic">Triticum aestivum L.</Emphasis>)

A set of 75 recombinant inbred lines (RILs) of the ITMI mapping population was grown under field conditions in Gatersleben. The lines were evaluated for the domestication traits pre-harvest sprouting and dormancy (germinability). Main QTLs could be localized for pre-harvest sprouting on chromosome 4AL and dormancy on chromosome 3AL. In addition, 85 Triticum aestivum cv. “Chinese Spring”-Aegilops tauschii introgression lines grown under greenhouse conditions were researched. No QTL could be found for pre-harvest sprouting but a major QTL could be detected for dormancy on chromosome 6DL.     

QTL analysis of quality traits in the spring wheat cross RL4452 × 'AC Domain'

Wheat grain quality is a complex group of traits of tremendous importance to wheat producers, end‐users and breeders. Quantitative trait locus (QTL) analysis studied the genetics of milling, mixograph, farinograph, baking, starch and noodle colour traits in the spring wheat population RL4452/‘AC Domain’. Forty‐seven traits were measured on the population and 99 QTLs were detected over 18 chromosomes for 41 quality traits. Forty‐four of these QTLs mapped to three major QTL clusters on chromosomes 1B, 4D, and 7D. Fourteen QTLs mapped near Glu‐B1, 20 QTLs mapped near a major plant height QTL on chromosome 4D, and 10 QTLs mapped near a major time to maturity QTL on chromosome 7D. Large QTLs were detected for grain and flour protein content, farinograph absorption, mixograph parameters, and dietary fibre on chromosome 2BS. QTLs for yellow alkaline noodle colour parameter L* mapped to chromosomes 5B and 5D, while the largest QTL for the b* parameter mapped to 7AL.     

Quantitative trait locus analysis of nitrogen use efficiency in barley (Hordeum vulgare L.)

Quantitative trait locus (QTL) analysis of nitrogen use efficiency (NUE) of barley (Hordeum vulgare L.) was conducted on data generated from two pot experiments carried out in 2005 (using four nitrogen rates) and 2008 (with three rates) with AFLP markers and 94 recombinant inbred lines (RILs) of the Prisma × Apex mapping population. In total 41 QTLs were detected on 6 chromosomes and for 18 traits in both trials. About 95 % of the detected QTLs were with major additive effects. The percentage of variance accounted for by individual QTLs in the multiple QTL mapping model ranged from 8.4 to 54.4 % across all mapped traits in both years. Fifteen QTLs were related to NUE and its components; most of these QTLs were detected at lower nitrogen rates and none at the highest rate in both trials. These QTLs were found on Chromosomes 3(3H) and 7(5H) in 2005 and Chromosome 2(2H) in 2008. Except for the QTLs of plant height and NUE based on grain yield, none of the QTLs which were detected for a given trait in 2005, expressed themselves in 2008 irrespective of the nitrogen levels. QTLs controlling some traits were co-located in each year, and QTLs for many traits were detected on the same chromosome and close to the denso locus. Further research is needed to investigate the possibility to reduce nitrogen fertilizer requirements through breeding while maintaining high yield of barley.     

Identification of a novel QTL for the number of spikelets per panicle using a cross between indica‐ and japonica‐type high‐yielding rice cultivars in Japan

Yield is a complex trait. To improve it, the accumulation of the favourable alleles of valuable genes is required for each yield‐related trait. In this study, we used two high‐yielding rice cultivars developed in Japan, indica‐type ‘Takanari’ and japonica‐type ‘Momiroman’, for a genetic analysis of the sink capacity‐related traits. An F₂ population showed transgressive segregation for the number of spikelets per panicle. Quantitative trait locus (QTL) analysis detected four QTLs for the trait. Two of the QTLs were most likely identical to previously cloned GN1a and APO1, and their Takanari alleles had positive effects. The Momiroman alleles of the other two QTLs had positive effects, and one of these QTLs was most likely identical to SPIKE/GPS. The QTL on the long arm of chromosome 3 appeared to be novel; it clustered with QTLs for grain length and days‐to‐heading. Substitution mapping revealed that the close linkage of QTLs caused the clustering. These results suggest that the combination of the favourable alleles of detected QTLs could lead to greater sink capacity than that of the parental cultivars.     

Genetic and QTL analyses of yield and a set of physiological traits in pepper

An interesting strategy for improvement of a complex trait dissects the complex trait in a number of physiological component traits, with the latter having hopefully a simple genetic basis. The complex trait is then improved via improvement of its component traits. As first part of such a strategy to improve yield in pepper, we present genetic and QTL analyses for four pepper experiments. Sixteen traits were analysed for a population of 149 recombinant inbred lines, obtained from a cross between the large-fruited pepper cultivar ‘Yolo Wonder’ (YW) and the small fruited pepper ‘Criollo de Morelos 334’ (CM334). The marker data consisted of 493 markers assembled into 17 linkage groups covering 1,775 cM. The trait distributions were unimodal, although sometimes skewed. Many traits displayed heterosis and transgression. Heritabilities were high (mean 0.86, with a range between 0.43 and 0.96). A multiple QTL mapping approach per trait and environment yielded 24 QTLs. The average numbers of QTLs per trait was two, ranging between zero and six. The total explained trait variance by QTLs varied between 9 and 61 %. QTL effects differed quantitatively between environments, but not qualitatively. For stem-related traits, the trait-increasing QTL alleles came from parent CM334, while for leaf and fruit related traits the increasing QTL alleles came from parent YW. The QTLs on linkage groups 1b, 2, 3a, 4, 6 and 12 showed pleiotropic effects with patterns that were consistent with the genetic correlations. These results contribute to a better understanding of the genetics of yield-related physiological traits in pepper and represent a first step in the improvement of the target trait yield.     

Identification of drought responsive QTLs during vegetative growth stage of rice using a saturated GBS-based SNP linkage map

Drought is a major abiotic constraint for rice production worldwide. The quantitative trait loci (QTLs) for drought tolerance traits identified in earlier studies have large confidence intervals due to low density linkage maps. Further, these studies largely focused on the above ground traits. Therefore, this study aims to identify QTLs for root and shoot traits at the vegetative growth stage using a genotyping by sequencing (GBS) based saturated SNP linkage map. A recombinant inbred line (RIL) population from a cross between Cocodrie and N-22 was evaluated for eight morphological traits under drought stress. Drought was imposed to plants grown in 75 cm long plastic pots at the vegetative growth stage. Using a saturated SNP linkage map, 14 additive QTLs were identified for root length, shoot length, fresh root mass, fresh shoot mass, number of tillers, dry root mass, dry shoot mass, and root-shoot ratio. Majority of the drought responsive QTLs were located on chromosome 1. The expression of QTLs varied under stress and irrigated condition. Shoot length QTLs qSL1.38 and qSL1.11 were congruent to dry shoot mass QTL qDSM1.38 and dry root mass QTL qDRM1.11, respectively. Analysis of genes present within QTL confidence intervals revealed many potential candidate genes such as laccase, Calvin cycle protein, serine threonine protein kinase, heat shock protein, and WRKY protein. Another important gene, Brevis radix, present in the root length QTL region, was known to modulate root growth through cell proliferation and elongation. The candidate genes and the QTL information will be helpful for marker-assisted pyramiding to improve drought tolerance in rice.     

Molecular mapping of QTLs for non-parasitic leaf spot resistance and comparison of half-sib DH populations in spring barley

Quantitative trait loci (QTLs) for resistance against non-parasitic leaf spots (NPLS) were first characterized in a spring barley double haploid population derived from the cross IPZ 24727/Barke (Behn et al., 2004). The aim of the present study was to identify QTLs for NPLS resistance in the half-sibling DH population IPZ 24727/Krona and to compare them with the QTLs of the population IPZ 24727/Barke. An anther culture-derived doubled haploid population of 536 DH lines was developed from the cross IPZ 24727 (resistant)/Krona (susceptible). Field trials were performed over two years in two replications, scoring NPLS and agronomic traits that might interact with NPLS. A molecular linkage map of 1035 cM was constructed based on AFLPs, SSRs and the mlo marker. QTL analyses for NPLS identified three QTLs that accounted for 30% of the phenotypic variation. For comparison of the QTLs from each DH population, a consensus map was generated comprising 277 markers with a length of 1199 cM. In both populations, the QTLs for NPLS mapped to chromosomes 1H, 4H and 7H. A common QTL with a great effect in both populations and over all environments was localized at the mlo locus on chromosome 4H, indicating that the mlo powdery mildew resistance locus has a considerable effect on NPLS susceptibility. The steps necessary to validate the QTLs and to improve the NPLS resistance by breeding were discussed.     

QTL analysis of cooked rice grain elongation, volume expansion, and water absorption using a recombinant inbred population

The traits of elongation, volume expansion, and water absorption are very important in determining the quality of cooked rice grains. In this study, quantitative trait loci (QTL) analysis of these traits was performed using a recombinant inbred population derived from a cross between two indica cultivars, ‘Zhenshan 97’ and ‘Minghui 63 ,’ which are the parents of the most widely grown hybrid rice in China. Using a linkage map based on 221 molecular marker loci covering a total of 1796 cM, a total of 33 QTLs were identified for the nine traits tested. QTLs were detected on chromosomes 1– 3 , 5– 9 , and 11 , respectively. The QTLs identified included three for cooked rice grain length elongation (chromosomes 2 , 6 , and 11), six for width expansion (chromosomes 1‐ 3 , 6 , 9 , and 11) and two for water absorption (chromosomes 2 and 6). Interestingly, a single QTL located near the wx gene on chromosome 6 seemed to influence all the traits tested for the cooked rice quality.     

Variation in heading date conceals quantitative trait loci for other traits of importance in breeding selection of rice

To identify quantitative trait loci (QTLs) associated with the primary target traits for selection in practical rice breeding programs, backcross inbred lines (BILs) derived from crosses between temperate japonica rice cultivars Nipponbare and Koshihikari were evaluated for 50 agronomic traits at six experimental fields located throughout Japan. Thirty-three of the 50 traits were significantly correlated with heading date. Using a linkage map including 647 single-nucleotide polymorphisms (SNPs), a total of 122 QTLs for 38 traits were mapped on all rice chromosomes except chromosomes 5 and 9. Fifty-eight of the 122 QTLs were detected near the heading date QTLs Hd16 and Hd17 and the remaining 64 QTLs were found in other chromosome regions. QTL analysis of 51 BILs having homozygous for the Koshihikari chromosome segments around Hd16 and Hd17 allowed us to detect 40 QTLs associated with 27 traits; 23 of these QTLs had not been detected in the original analysis. Among the 97 QTLs for the 30 traits measured in multiple environments, the genotype-by-environment interaction was significant for 44 QTLs and not significant for 53 QTLs. These results led us to propose a new selection strategy to improve agronomic performance in temperate japonica rice cultivars.     

水稻根系性状QTL的整合、分类和真实性分析

为提高水稻根系性状QTL 分子标记辅助选择利用效率, 利用饱和分子标记连锁图谱,对已发表的水旱稻根系性状QTL进行了整合,并对这些QTL的贡献率、分布特点和真实性进行了分析。结果如下：通过对QTL贡献率分析得到11个主效QTL;根据QTL在染色体上的位置,确定1,2,3,5,11号染色体上共11个分子标记区域为“一因多效”可能性较大区域;通过对这些QTL的真实性分析共得到35个“真实”QTL和3个“热点”QTL。这些主效QTL、成簇分布QTL及“热点” QTL可作为水稻根系性状分子育种的重要候选区域。     

Identification of quantitative trait loci (QTLs) associated with maintenance of wheat (Triticum aestivum Desf.) quality characteristics under heat stress conditions

The goal of this study was to identify quantitative trait loci (QTLs) associated with the maintenance of wheat grain quality following post-anthesis heat stress in a recombinant inbred line (RIL) population. The response to heat stress was measured using the sodium dodecyl sulfate sedimentation test (SDSS), a significant predictor of bread baking quality. SDSS scores were used to identify QTLs associated with grain quality and QTLs associated with quality stability were identified based on percent change in SDSS score between the heat stress and control treatments. Four QTLs were identified, located one each on linkage groups 1B, 1D, 4A, and 7A. The 1B, 1D, and 4A QTLs were associated with grain quality; the QTL on linkage group 7A was associated with quality stability. To confirm the detected QTLs, eighty advanced lines grown at three Texas nurseries were tested for relationships between allelic polymorphism at QTL linked markers and quality traits. Quality trait stability in the advanced lines was estimated using the coefficient of variability (CV%) of quality traits between nurseries. The analysis supported the relationship of the predicted QTLs on linkage groups 1B, 1D, and 4A with quality traits. The confirmed QTLs may be used in marker assisted selection (MAS) to develop wheat lines possessing superior quality traits. In addition, identification of genetic regions associated with this trait will aid the identification of the underlying genes.