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1.
The objective of this study was to dissect the genetic control of days to flowering (DTF) and photoperiod sensitivity (PS) into the various components including the main-effect quantitative trait loci (QTLs), epistatic QTLs and QTL-by-environment interactions (QEs). Doubled haploid (DH) fines were produced from an F1 between two spring Brassica napus cultivars Hyola 401 and Q2. DTF of the DH lines and parents were investigated in two locations, one location with a short and the other with a long photoperiod regime over two years. PS was calculated by the delay in DTF under long day as compared to that under short day. A genetic linkage map was constructed that comprised 248 marker loci including SSR, SRAP and AFLP markers. Further QTL analysis resolved the genetic components of flowering time and PS into the main-effect QTLs, epistatic QTLs and QEs. A total of 7 main-effect QTLs and 11 digenic interactions involving 21 loci located on 13 out of the 19 linkage groups were detected for the two traits. 3 main-effect QTLs and 4 pairs of epistatic QTLs were involved in QEs conferring DTF. One QTL on linkage group (LG) 18 was revealed to simultaneously affect DTF and PS and explain for the highest percentage of the phenotypic variation. The implications of the results for B. napus breeding have been discussed. 相似文献
2.
The objective of this study was to dissect the genetic control of days to flowering (DTF) and photoperiod sensitivity (PS)
into the various components including the main-effect quantitative trait loci (QTLs), epistatic QTLs and QTL-by-environment
interactions (QEs). Doubled haploid (DH) lines were produced from an F1 between two spring Brassica napus cultivars Hyola 401 and Q2. DTF of the DH lines and parents were investigated in two locations, one location with a short
and the other with a long photoperiod regime over two years. PS was calculated by the delay in DTF under long day as compared
to that under short day. A genetic linkage map was constructed that comprised 248 marker loci including SSR, SRAP, and AFLP
markers. Further QTL analysis resolved the genetic components of flowering time and PS into the main-effect QTLs, epistatic
QTLs, and QEs. A total of 7 main-effect QTLs and 11 digenic interactions involving 21 loci located on 13 out of the 19 linkage
groups were detected for the two traits. Three main-effect QTLs and four pairs of epistatic QTLs were involved in QEs conferring
DTF. One QTL on linkage group (LG) 18 was revealed to simultaneously affect DTF and PS and explain for the highest percentage
of the phenotypic variation. The implications of the results for B. napus breeding have been discussed.
The text was submitted by the authors in English. 相似文献
3.
Jiang GH He YQ Xu CG Li XH Zhang Q 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2004,108(4):688-698
Delayed leaf-senescence, or stay-green, has been regarded as a desired characteristic for the production of a number of crops including rice. In this study, we analyzed the genetic basis of stay-green using a population of 190 doubled haploid lines from the cross between an indica parent Zhenshan 97 and a stay-green japonica parent Wuyujing 2. The population was tested in replicated field trials in 2 consecutive years, and six traits were defined to evaluate the stay-green characteristics. A genetic linkage map with 179 SSR (simple sequence repeat) marker loci was constructed. The software QTLMapper, based on a mixed linear model approach, was applied to detect QTLs, epistatic effects and their environmental interactions for these traits. A total of 46 main-effect QTLs was detected for the six traits that can be localized to 25 chromosomal regions. The individual effects of all the QTLs were small. Fifty digenic interactions were resolved that involved 66 loci distributed on all 12 chromosomes. Environmental interactions were detected for 18 of the main-effect QTLs and 14 of the epistatic interactions. Collectively, the epistatic effects and QTL by year interactions accounted for large proportions of the phenotypic variations. The results also showed that most of the stay-green traits were negatively correlated with yield and its component traits. The implications of the results in crop improvement were discussed.Communicated by C. Möllers 相似文献
4.
Epistatic interaction is an important genetic basis of grain yield and its components in maize 总被引:4,自引:0,他引:4
X. Q. Ma J. H. Tang W. T. Teng J. B. Yan Y. J. Meng J. S. Li 《Molecular breeding : new strategies in plant improvement》2007,20(1):41-51
A population of 294 recombinant inbred lines (RIL) derived from Yuyu22, an elite maize hybrid extending broadly in China,
has been constructed to investigate the genetic basis of grain yield, and associated yield components in maize. The main-effect
quantitative trait loci (QTL), digenic epistatic interactions, and their interactions with the environment for grain yield
and its three components were identified by using the mixed linear model approach. Thirty-two main-effect QTL and forty-four
pairs of digenic epistatic interactions were detected for the four measured traits in four environments. Our results suggest
that both additive effects and epistasis (additive × additive) effects are important genetic bases of grain yield and its
components in the RIL population. Only 30.4% of main-effect QTL for ear length were involved in epistatic interactions. This
implies that many loci in epistatic interactions may not have significant effects for traits alone but may affect trait expression
by epistatic interaction with the other loci. 相似文献
5.
The main effects, epistatic effects and environmental interactions of QTLs on the cooking and eating quality of rice in a doubled-haploid line population 总被引:12,自引:0,他引:12
Fan CC Yu XQ Xing YZ Xu CG Luo LJ Zhang Q 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2005,110(8):1445-1452
Amylose content (AC), gel consistency (GC) and gelatinazation temperature (GT) are three important traits that influence the cooking and eating quality of rice. The objective of this study was to characterize the genetic components, including main-effect quantitative trait loci (QTLs), epistatic QTLs and QTL-by-environment interactions (QEs), that are involved in the control of these three traits. A population of doubled haploid (DH) lines derived from a cross between two indica varieties Zhenshan 97 and H94 was used, and data were collected from a field experiment conducted in two different environments. A genetic linkage map consisting of 218 simple sequence repeat (SSR) loci was constructed, and QTL analysis performed using qtlmapper 1.6 resolved the genetic components into main-effect QTLs, epistatic QTLs and QEs. The analysis detected a total of 12 main-effect QTLs for the three traits, with a QTL corresponding to the Wx locus showing a major effect on AC and GC, and a QTL corresponding to the Alk locus having a major effect on GT. Ten digenic interactions involving 19 loci were detected for the three traits, and six main-effect QTLs and two pairs of epistatic QTLs were involved in QEs. While the main-effect QTLs, especially the ones corresponding to known major loci, apparently played predominant roles in the genetic basis of the traits, under certain conditions epistatic effects and QEs also played important roles in controlling the traits. The implications of the findings for rice quality improvement are discussed. 相似文献
6.
利用双单倍体群体剖析水稻产量及其相关性状的遗传基础 总被引:23,自引:0,他引:23
主效QTL、上位性效应和它们与环境的互作(QE)都是数量性状的重要遗传因素。利用籼粳交珍汕97/武育粳2号F1植株上的花药进行组织培养得到的190个双单倍体群体和179个微卫星标记,通过两年两重复田间试验,采用混合线性模型方法分析了9个控制水稻产量及其相关性状的遗传效应,得到57个主效QTL,41对上位性互作,8对QTL与环境的互作和7对上位性效应与环境的互作。单个主效QTL解释这些性状1.3%~25.8%的表型方差。各性状QTL的累积表型贡献率达11.5%~66.8%。大多数性状之间具有显著的表型相关性,相关性较高的性状之间常具有较多共同或紧密连锁的QTL。结果表明,基因的多效性或紧密连锁可能是性状相关的重要遗传基础。 相似文献
7.
Xiaojing Dang Thu Giang Tran Thi Guanshan Dong Hui Wang Wisdom Mawuli Edzesi Delin Hong 《Planta》2014,239(6):1309-1319
Key message
Twenty-seven QTLs were identified for rice seed vigor, in which 16 were novel QTLs. Fifteen elite parental combinations were designed for improving seed vigor in rice.Abstract
Seed vigor is closely related to direct seeding in rice (Oryza sativa L.). Previous quantitative trait locus (QTL) studies for seed vigor were mainly derived from bi-parental segregating populations and no report from natural populations. In this study, association mapping for seed vigor was performed on a selected sample of 540 rice cultivars (419 from China and 121 from Vietnam). Population structure was estimated on the basis of 262 simple sequence repeat (SSR) markers. Seed vigor was evaluated by root length (RL), shoot length (SL) and shoot dry weight in 2011 and 2012. Abundant phenotypic and genetic diversities were found in the studied population. The population was divided into seven subpopulations, and the levels of linkage disequilibrium (LD) ranged from 10 to 80 cM. We identified 27 marker–trait associations involving 18 SSR markers for three traits. According to phenotypic effects for alleles of the detected QTLs, elite alleles were mined. These elite alleles could be used to design parental combinations and the expected results would be obtained by pyramiding or substituting the elite alleles per QTL (apart from possible epistatic effects). Our results demonstrate that association mapping can complement and enhance previous QTL information for marker-assisted selection and breeding by design. 相似文献8.
Grain chalkiness is one of the important appearance qualities in rice marketing. But it is a complex trait, controlled by polygenes and easily influenced by the environment. Genetic analysis and QTL detection was carried out on six characteristics of grain chalkiness consisting of the percentage of chalkiness (PGC), white belly (PWB) and white core grains (PWC), and the area of chalkiness (CA), white belly (WBA) and white core (WCA) in brown rice. A total of 16 main-effect QTLs associated with chalkiness characteristics of brown rice were mapped on seven chromosomes over two years. Among them,qPGC7.1 andqPWB7.2 were simultaneously located on chromosome 7 flanked by 7038 and 7042 at LOD scores 4.34 and 3.76, whileqPWC2.1 andqWCA2.1 were simultaneously located on chromosome 2 flanked by RM492 and RM324 with LOD scores of 2.50 and 3.39. Twelve epistatic combinations were detected for five chalkiness characteristics except for CA. Results indicated that WBA was mainly influenced by the additive effects of main-effect QTLs. PGC and PWC were affected by the effects of epistatic QTLs and the interactions between additive-by-additive effects and the environment. The effects of epistatic QTLs and the main-effect QTLs played important roles on CA, PWB and WCA. For the genetic improvement of grain chalkiness in breeding system, more attention should be paid to epistatic effects and the additive effects of main-effect QTLs. 相似文献
9.
The concentration of protein in soybean is an important trait that drives successful soybean quality. A recombinant inbred line derived from a cross between the Charleston and Dongnong594 cultivars was planted in one location across 10 years and two locations across 5 years in China (20 environments in total), and the genetic effects were partitioned into additive main effects, epistatic main effects and their environmental interaction effects using composite interval mapping and inclusive composite interval mapping models based on a high-density genetic map. Ten main-effect quantitative trait loci (QTLs) were identified on chromosomes 3, 6, 7, 13, 15 and 20 and detected in more than three environments, with each of the main-effect QTLs contributing a phenotypic variation of around 10 %. Between the intervals of the main-effect QTLs, 93 candidate genes were screened for their involvement in seed protein storage and/or amino acid biosynthesis and metabolism processes based on gene ontology and annotation information. Furthermore, an analysis of epistatic interactions showed that three epistatic QTL pairs were detected, and could explain approximately 50 % of the phenotypic variation. The additive main-effect QTLs and epistatic QTL pairs contributed to high phenotypic variation under multiple environments, and the results were also validated and corroborated with previous research, indicating that marker-assisted selection can be used to improve soybean protein concentrations and that the candidate genes can also be used as a foundation data set for research on gene function. 相似文献
10.
Many important phenotypic traits in plants are ordinal. However, relatively little is known about the methodologies for ordinal trait association studies. In this study, we proposed a hierarchical generalized linear mixed model for mapping quantitative trait locus (QTL) of ordinal traits in crop cultivars. In this model, all the main-effect QTL and QTL-by-environment interaction were treated as random, while population mean, environmental effect and population structure were fixed. In the estimation of parameters, the pseudo data normal approximation of likelihood function and empirical Bayes approach were adopted. A series of Monte Carlo simulation experiments were performed to confirm the reliability of new method. The result showed that new method works well with satisfactory statistical power and precision. The new method was also adopted to dissect the genetic basis of soybean alkaline-salt tolerance in 257 soybean cultivars obtained, by stratified random sampling, from 6 geographic ecotypes in China. As a result, 6 main-effect QTL and 3 QTL-by-environment interactions were identified. 相似文献
11.
Yogendra Khedikar Manish K. Pandey V. Sujay Sube Singh Spurthi N. Nayak Henry W. Klein-Gebbinck Cholin Sarvamangala Ganapati Mukri Vanika Garg Hari D. Upadhyaya H. L. Nadaf M. V. C. Gowda Rajeev K. Varshney Ramesh S. Bhat 《Molecular breeding : new strategies in plant improvement》2018,38(1):7
An effort was made in the present study to identify the main effect and epistatic quantitative trait locus (QTL) for the morphological and yield-related traits in peanut. A recombinant inbred line (RIL) population derived from TAG 24 × GPBD 4 was phenotyped in seven environments at two locations. QTL analysis with available genetic map identified 62 main-effect QTLs (M-QTLs) for ten morphological and yield-related traits with the phenotypic variance explained (PVE) of 3.84–15.06%. Six major QTLs (PVE >?10%) were detected for PLHT, PPP, YPP, and SLNG. Stable M-QTLs appearing in at least two environments were detected for PLHT, LLN, YPP, YKGH, and HSW. Five M-QTLs governed two traits each, and 16 genomic regions showed co-localization of two to four M-QTLs. Intriguingly, a major QTL reported to be linked to rust resistance showed pleiotropic effect for yield-attributing traits like YPP (15.06%, PVE) and SLNG (13.40%, PVE). Of the 24 epistatic interactions identified across the traits, five interactions involved six M-QTLs. Three interactions were additive × additive and remaining two involved QTL × environment (QE) interactions. Only one major M-QTL governing PLHT showed epistatic interaction. Overall, this study identified the major M-QTLs for the important productivity traits and also described the lack of epistatic interactions for majority of them so that they can be conveniently employed in peanut breeding. 相似文献
12.
Tianzhen Zhang Neng Qian Xiefei Zhu Hong Chen Sen Wang Hongxian Mei Yuanming Zhang 《PloS one》2013,8(2)
Cotton is the world’s leading cash crop, and genetic improvement of fiber yield and quality is the primary objective of cotton breeding program. In this study, we used various approaches to identify QTLs related to fiber yield and quality. Firstly, we constructed a four-way cross (4WC) mapping population with four base core cultivars, Stoneville 2B, Foster 6, Deltapine 15 and Zhongmiansuo No.7 (CRI 7), as parents in Chinese cotton breeding history and identified 83 QTLs for 11 agronomic and fiber quality traits. Secondly, association mapping of agronomical and fiber quality traits was based on 121 simple sequence repeat (SSR) markers using a general linear model (GLM). For this, 81 Gossypium hirsutum L. accessions including the four core parents and their derived cultivars were grown in seven diverse environments. Using these approaches, we successfully identified 180 QTLs significantly associated with agronomic and fiber quality traits. Among them were 66 QTLs that were identified via linkage disequilibrium (LD) and 4WC family-based linkage (FBL) mapping and by previously published family-based linkage (FBL) mapping in modern Chinese cotton cultivars. Twenty eight and 44 consistent QTLs were identified by 4WC and LD mapping, and by FBL and LD mapping methods, respectively. Furthermore, transmission and variation of QTL-alleles mapped by LD association in the three breeding periods revealed that some could be detected in almost all Chinese cotton cultivars, suggesting their stable transmission and some identified only in the four base cultivars and not in the modern cultivars, suggesting they were missed in conventional breeding. These results will be useful to conduct genomics-assisted breeding effectively using these existing and novel QTL alleles to improve yield and fiber qualities in cotton. 相似文献
13.
QTLs for low nitrogen tolerance at seedling stage identified using a recombinant inbred line population derived from an elite rice hybrid 总被引:9,自引:0,他引:9
Lian X Xing Y Yan H Xu C Li X Zhang Q 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2005,112(1):85-96
Tolerance to low nitrogen conditions is a highly desired characteristic for sustainable crop production. In this study, we analyzed the genetic components associated with low N tolerance in rice at seedling stage, including main effects, epistatic effects of the quantitative trait locus (QTLs), and QTL by environment interactions (QEs), using a population of 239 recombinant inbred lines (RILs) from a cross between Zhenshan 97 and Minghui 63, the parents of an elite hybrid. A genetic linkage map with 253 DNA maker loci was constructed. Seedlings of RILs were cultivated in low N and normal N solutions. Root, shoot and plant weight in the two N treatments were measured and the relative weight of the two treatments for each trait was considered as measurements for low N tolerance. Four to eight QTLs with main effects were detected for each of the nine traits. Very few QTLs were detected in both low and normal N conditions, and most QTLs for the relative measurements were different from those for traits under the two N treatments, indicating very little commonality in the genetic basis of the traits and their relative performance under low and normal N conditions. A total of 103 digenic interactions were detected for the nine traits. While the epistatic effects collectively accounted for large proportions of the variation for several traits, the effects of QEs appeared to be trivial. It was concluded that low N tolerance of rice seedling had complex genetic basis that requires extensive studies for full characterization. 相似文献
14.
Würschum T Maurer HP Kraft T Janssen G Nilsson C Reif JC 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2011,123(7):1121-1131
Recent results indicate that association mapping in populations from applied plant breeding is a powerful tool to detect QTL
which are of direct relevance for breeding. The focus of this study was to unravel the genetic architecture of six agronomic
traits in sugar beet. To this end, we employed an association mapping approach, based on a very large population of 924 elite
sugar beet lines from applied plant breeding, fingerprinted with 677 single nucleotide polymorphism (SNP) markers covering
the entire genome. We show that in this population linkage disequilibrium decays within a short genetic distance and is sufficient
for the detection of QTL with a large effect size. To increase the QTL detection power and the mapping resolution a much higher
number of SNPs is required. We found that for QTL detection, the mixed model including only the kinship matrix performed best,
even in the presence of a considerable population structure. In genome-wide scans, main effect QTL and epistatic QTL were
detected for all six traits. Our full two-dimensional epistasis scan revealed that for complex traits there appear to be epistatic
master regulators, loci which are involved in a large number of epistatic interactions throughout the genome. 相似文献
15.
Jung-Hyun Lim Hyun-Jung Yang Ki-Hong Jung Soo-Cheul Yoo Nam-Chon Paek 《Molecules and cells》2014,37(2):149-160
Plant breeders have focused on improving plant architecture as an effective means to increase crop yield. Here, we identify the main-effect quantitative trait loci (QTLs) for plant shape-related traits in rice (Oryza sativa) and find candidate genes by applying whole genome re-sequencing of two parental cultivars using next-generation sequencing. To identify QTLs influencing plant shape, we analyzed six traits: plant height, tiller number, panicle diameter, panicle length, flag leaf length, and flag leaf width. We performed QTL analysis with 178 F7 recombinant in-bred lines (RILs) from a cross of japonica rice line ‘SNUSG1’ and indica rice line ‘Milyang23’. Using 131 molecular markers, including 28 insertion/deletion markers, we identified 11 main- and 16 minor-effect QTLs for the six traits with a threshold LOD value > 2.8. Our sequence analysis identified fifty-four candidate genes for the main-effect QTLs. By further comparison of coding sequences and meta-expression profiles between japonica and indica rice varieties, we finally chose 15 strong candidate genes for the 11 main-effect QTLs. Our study shows that the whole-genome sequence data substantially enhanced the efficiency of polymorphic marker development for QTL fine-mapping and the identification of possible candidate genes. This yields useful genetic resources for breeding high-yielding rice cultivars with improved plant architecture. 相似文献
16.
Characterization of the main effects,epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice 总被引:35,自引:0,他引:35
Xing Z Tan F Hua P Sun L Xu G Zhang Q 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2002,105(2-3):248-257
Main effects, epistatic effects and their environmental interactions of QTLs are all important genetic components of quantitative traits. In this study, we analyzed the main effects, epistatic effects of the QTLs, and QTL by environment interactions (QEs) underlying four yield traits, using a population of 240 recombinant inbred lines from a cross between two rice varieties tested in replicated field trials. A genetic linkage map with 220 DNA marker loci was constructed. A mixed linear model approach was used to detect QTLs with main effects, QTLs involved in digenic interactions and QEs. In total, 29 QTLs of main effects, and 35 digenic interactions involving 58 loci were detected for the four traits. Thirteen QTLs with main effects showed QEs; no QE was detected for the QTLs involved in epistatic interactions. The amount of variations explained by the QTLs of main effect were larger than the QTLs involved in epistatic interactions, which in turn were larger than QEs for all four traits. This study illustrates the ability of the analysis to assess the genetic components underlying the quantitative traits, and demonstrates the relative importance of the various components as the genetic basis of yield traits in this population. 相似文献
17.
Yuan Niu Yu Xu Xiao-Fen Liu Sheng-Xian Yang Shi-Ping Wei Fang-Teng Xie Yuan-Ming Zhang 《Molecular breeding : new strategies in plant improvement》2013,31(4):785-794
Seed size and shape traits are closely related to seed yield and appearance quality in soybean (Glycine max L.). Previous studies were mainly derived from bi-parental segregating populations and relatively little is known about the results in soybean cultivars. In this study, 257 soybean cultivars obtained by stratified random sampling from six geographic ecotypes in China were used to carry out association mapping for these traits using information from 135 simple sequence repeat markers and an epistatic association mapping approach implemented using an empirical Bayes algorithm. In this analysis, seed size was measured by seed length (SL), width (SW) and thickness (ST), and seed shape was evaluated by seed length-to-width (SLW), length-to-thickness (SLT) and width-to-thickness (SWT) ratios, in 2008–2010. A total of 59 main-effect quantitative trait loci (QTL) and 31 QTL-by-environment interactions were identified. Among them, 25 QTL were associated simultaneously with at least two traits; 80 QTL (90 %) could be confirmed by enriched compression mixed linear model analysis; and the size for a large number of detected QTL was minor, except for qSL-5, qSW-7e, qST-5-2 and qSLW-2. According to the estimates for the allelic effects of the detected QTL, elite alleles could be mined: for example, the 307-bp allele of QTL linked to satt453 was the best for seed length. These elite alleles could be used to design parental combinations; e.g., the cross of Zhenghezhibanzi and Nannongdahuangdou might improve seed length, and the combination of cultivars Lindou10, Deqingxiangzhudou, Ninghaixiazhidou, Zhenghezhibanzi, 0803, Shangqiu7605 and 0831 might pyramid 42 elite alleles. 相似文献
18.
Elsayed Mansour Ana M. Casas M. Pilar Gracia José Luis Molina-Cano Marian Moralejo Luigi Cattivelli William T. B. Thomas Ernesto Igartua 《Molecular breeding : new strategies in plant improvement》2014,33(2):249-265
Advances in plant breeding through marker-assisted selection (MAS) are only possible when genes or quantitative trait loci (QTLs) can contribute to the improvement of elite germplasm. A population of recombinant inbred lines (RILs) was developed for one of the best crosses of the Spanish National Barley Breeding Program, between two six-row winter barley cultivars Orria and Plaisant. The objective of this study was to identify favourable QTLs for agronomic traits in this population, which may help to optimise breeding strategies for these and other elite materials for the Mediterranean region. A genetic linkage map was developed for 217 RILs, using 382 single nucleotide polymorphism markers, selected from the barley oligonucleotide pool assay BOPA1 and two genes. A subset of 112 RILs was evaluated for several agronomic traits over a period of 2 years at three locations, Lleida and Zaragoza (Spain) and Fiorenzuola d’Arda (Italy), for a total of five field trials. An important segregation distortion occurred during population development in the region surrounding the VrnH1 locus. A QTL for grain yield and length of growth cycle was also found at this locus, apparently linked to a differential response of the VrnH1 alleles to temperature. A total of 33 QTLs was detected, most of them for important breeding targets such as plant height and thousand-grain weight. QTL × environment interactions were prevalent for most of the QTLs detected, although most interactions were of a quantitative nature. Therefore, QTLs suitable for MAS for most traits were identified. 相似文献
19.
20.
Fernando J. Yuste-Lisbona Ana M. González Carmen Capel Manuel García-Alcázar Juan Capel Antonio M. De Ron Rafael Lozano Marta Santalla 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2014,127(4):897-912