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1.
Tiller number per plant (TN) and plant height (PH) are important agronomic traits related to grain yield (GY) in rice (Oryza sativa L.). A total of 30 additive quantitative trait loci (A-QTL) and 9 significant additive × environment interaction QTLs (AE-QTL) were detected, while the phenotypic and QTL correlations confirmed the intrinsic relationship of the three traits. These QTLs were integrated with 986 QTLs from previous studies by metaanalysis. Consensus maps contained 7156 markers for a total map length of 1112.71 cM, onto which 863 QTLs were projected; 78 meta-QTLs (MQTLs) covering 11 of the 30 QTLs were detected from the cross between Dongnong422 and Kongyu131 in this study. A total of 705 predicted genes were distributed over the 21 MQTL intervals with physical length <0.3 Mb; 13 of the 21 MQTLs, and 34 candidate genes related to grain yield and plant development, were screened. Five major QTLs, viz. qGY6-2, qPH7-2, qPH6-3, qTN6-1, and qTN7-1, were not detected in the MQTL intervals and could be used as newly discovered QTLs. Candidate genes within these QTL intervals will play a meaningful role in molecular marker-assisted selection and map-based cloning of rice TN, PH, and GY.  相似文献   

2.
To better understand the underlying mechanisms of agronomic traits related to drought resistance and discover candidate genes or chromosome segments for drought-tolerant rice breeding, a fundamental introgression population, BC3, derived from the backcross of local upland rice cv. Haogelao (donor parent) and super yield lowland rice cv. Shennong265 (recurrent parent) had been constructed before 2006. Previous quantitative trait locus (QTL) mapping results using 180 and 94 BC3F6,7 rice introgression lines (ILs) with 187 and 130 simple sequence repeat (SSR) markers for agronomy and physiology traits under drought in the field have been reported in 2009 and 2012, respectively. In this report, we conducted further QTL mapping for grain yield component traits under water-stressed (WS) and well-watered (WW) field conditions during 3 years (2012, 2013 and 2014). We used 62 SSR markers, 41 of which were newly screened, and 492 BC4F2,4 core lines derived from the fourth backcross between D123, an elite drought-tolerant IL (BC3F7), and Shennong265. Under WS conditions, a total of 19 QTLs were detected, all of which were associated with the new SSRs. Each QTL was only identified in 1 year and one site except for qPL-12-1 and qPL-5, which additively increased panicle length under drought stress. qPL-12-1 was detected in 2013 between new marker RM1337 and old marker RM3455 (34.39 cM) and was a major QTL with high reliability and 15.36% phenotypic variance. qPL-5 was a minor QTL detected in 2013 and 2014 between new marker RM5693 and old marker RM3476. Two QTLs for plant height (qPHL-3-1 and qPHP-12) were detected under both WS and WW conditions in 1 year and one site. qPHL-3-1, a major QTL from Shennong265 for decreasing plant height of leaf located on chromosome 3 between two new markers, explained 22.57% of phenotypic variation with high reliability under WS conditions. On the contrary, qPHP-12 was a minor QTL for increasing plant height of panicle from Haogelao on chromosome 12. Except for these two QTLs, all other 17 QTLs mapped under WS conditions were not mapped under WW conditions; thus, they were all related to drought tolerance. Thirteen QTLs mapped from Haogelao under WS conditions showed improved drought tolerance. However, a major QTL for delayed heading date from Shennong265, qDHD-12, enhanced drought tolerance, was located on chromosome 12 between new marker RM1337 and old marker RM3455 (11.11 cM), explained 21.84% of phenotypic variance and showed a negative additive effect (shortening delay days under WS compared with WW). Importantly, chromosome 12 was enriched with seven QTLs, five of which, including major qDHD-12, congregated near new marker RM1337. In addition, four of the seven QTLs improved drought resistance and were located between RM1337 and RM3455, including three minor QTLs from Haogelao for thousand kernel weight, tiller number and panicle length, respectively, and the major QTL qDHD-12 from Shennong265. These results strongly suggested that the newly screened RM1337 marker may be used for marker-assisted selection (MAS) in drought-tolerant rice breeding and that there is a pleiotropic gene or cluster of genes linked to drought tolerance. Another major QTL (qTKW-1-2) for increasing thousand kernel weight from Haogelao was also identified under WW conditions. These results are helpful for MAS in rice breeding and drought-resistant gene cloning.  相似文献   

3.
Plant height determines plant biomass yield, harvest index and economic yield. We analyzed quantitative trait loci (QTL) and gene action controlling plant height. We generated the maternal and paternal testcrossing (TC/M and TC/P) populations based on a recombinant inbred line population. Data for plant height at t1, t2, t3, t4 or t5 stages were collected over 2 years from 3 TC/M field trials and 2 TC/P field trials. At single-locus level, 32 QTLs at five stages and 24 conditional QTLs at four intervals were detected, and 14 QTLs shared in different years or populations or stages. Plant height displayed dynamic characteristics through expression of QTLs. A total of 21 novel QTLs were detected and 11 QTLs validated the previous results. And 19 QTLs explained over 10% of phenotypic variation, such as qPH-Chr9-2, qPH-Chr19-4 and qPH-Chr22-4. The region of NAU5330-NAU1269 on chromosome 19 may be a desired target for genetic improvement of plant height in Upland cotton. In addition, five and eight heterotic loci were identified in TC/M and TC/P populations, respectively. Additive, partial dominance and overdominance effects were observed in both TC populations. We also identified 43 epistatic QTLs and QTLs by environment interactions by inclusive composite interval mapping method. Taken together, additive, partial dominance and overdominance effects together with epistasis explained the genetic basis of plant height in Upland cotton.  相似文献   

4.
The ongoing rise in temperatures caused by global climate change is a critical climatic risk factor for rice production, and enhancing rice heat tolerance is an area of particular research interest. A recombinant inbred line (RIL) mapping population was developed from heat sensitive, rice cultivar IAPAR-9 crossed with heat tolerant, Liaoyan241. RIL and parental lines were exposed to high temperature at the heating and flowering stage in experiments in 2014 and 2015. As indicators of heat tolerance, the seed setting rate under natural (NS) and heat stress (HTS) conditions were measured, and the reduction rate of seed set (RRS) was calculated. Quantitative trait loci (QTL) analysis revealed eleven heat tolerance QTLs located on chromosomes 1, 3, 4, 5, and 6. Single QTL contribution rates were 4.75–13.81% and effect values were ? 5.98 to 5.00. Four major QTLs (qNS1, qNS4, qNS6, and qRRS1) were stable detected in different environments in both years. Thirteen QTLs with epistatic interactions and nine QTLs with environmental interactions were also detected. Major QTLs were all involved in epistatic and environmental interactions. Three QTLs from the SSR marker interval RM471 to RM177 region of chromosome 4 (qNS4, qHTS4, and qRRS4) were all involved in epistatic and environmental interactions and contributed to phenotypic variation, indicating that this region constituted a major QTL hotspot. The major QTL for heat tolerance identified in this study will aid in breeding tolerant cultivars and facilitating investigation of the molecular underpinnings of heat tolerance in rice.  相似文献   

5.
Grain weight and grain length are the most stable components of rice yield and important indicators of consumer preference. Considering the potentials of wild rice and to enhance the rice yields to meet the increasing demands, 185 Backcross Inbred Lines (BILs) in the background of O. sativa ssp. indica cv. PR114, including 63 rufi-BILs derived from O. rufipogon IRGC104433 and 122 glumae-BILs from O. glumaepatula IRGC104387 were evaluated for mapping QTLs for yield and yield component traits using Genotyping by Sequencing (GBS). Phenotypic evaluation of BILs in three seasons spanning two locations revealed significant differences compared with recurrent parent. BILs which did not show significant differences for any trait under investigation, or similar based on pedigree, were excluded from GBS. Some glumae-BILs had to be excluded from mapping QTLs due to less sequence information. A custom designed approach for GBS data analysis identified 3322 informative SNPs in 55 rufi-BILs and 3437 informative SNPs in 79 glumae-BILs. QTL mapping identified one QTL for thousand grain weight (qtgw5.1), two for grain width (qgw5.1, qgw5.2) and one for grain length (qgl7.1) in rufi-BILs. In the glumae-BILs, three QTL for thousand grain weight (qtgw2.1, qtgw3.1, qtgw6.1) and two for grain length (qgl3.1, qgl7.1) were identified. Most of the grain weight and width QTL showed positive additive effect contributed by wild species allele, whereas the grain length QTL showed positive additive effect contributed by recurrent parent allele. Based on their physical position, none of the QTLs were found similar to previously cloned QTLs. QTLs for grain traits identified from low yielding wild relatives of rice reveals their significance in improving further the rice yields and widen the genetic base of cultivated rice.  相似文献   

6.
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7.
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.  相似文献   

8.
Soybean is a primary source of plant oil and protein and has a high nutritional value. Plant height (PH) and flowering time (FT) are two important agronomic traits in breeding programs for soybean. In this study, we mapped QTLs associated with PH and FT in three environments using a population with determinate growth including 236 recombinant inbred lines (NJZY-RIL) derived from a cross between two summer planting varieties, ZXD and NN1138-2. A high-density genetic map with 3255 SLAF-markers was constructed that spanned 2144.85 cM of the soybean genome with an average marker distance of 0.66 cM. Altogether, six QTLs controlling PH and eleven QTLs controlling FT were mapped using mixed-model-based composite interval mapping and composite interval mapping methods. qPH-1-1 and qFT-15-2 were two novel main effect QTLs identified in this study; qFT-6-2, qFT-15-2, qFT-16-1, qPH-1-1, qPH-15-1 and qPH-16-1 were consistently detected across environments and by the two mapping methods. Two pairs of QTLs, qFT-15-2 and qPH-15-1 as well as qFT-16-1 and qPH-16-1, which were located in the same marker interval on chromosomes 15 and 16, respectively, were found to have close linkage or pleiotropy. These results may increase our understanding of the genetic control of PH and FT in soybean and provide support for implementing marker-assisted selection in developing soybean cultivars with high yield and early maturity in summer planting regions.  相似文献   

9.
Previous studies reported that some genotypes with introgressed Festuca chromosome segment(s) in Lolium genome showed enhanced winter hardiness compared to Lolium. The aim of this study was to search comprehensively for the Festuca pratensis chromosome regions affecting winter hardiness-related traits when introgressed into the Lolium perenne genome. Association between F. pratensis introgression and winter hardiness-related traits (fall and winter hardiness indexes, early-spring dry matter yield, and freezing tolerance) were screened in the diploid introgression populations (n = 203) that had some F. pratensis chromosome segments introgressed. Eighty-four intron markers corresponding to unique rice genes randomly distributed across the genome were used for genotyping. Winter hardiness of almost all plants in the introgression populations was lower than that of the F. pratensis and triploid hybrid parents, but the average was higher than that of L. perenne. A significant positive effect of F. pratensis introgression on early-spring dry matter yield was detected on chromosome 7. This quantitative trait locus (QTL) was confirmed by linkage analysis using a backcross population with F. pratensis introgression in the target region of chromosome 7. However, the contribution of the newly identified QTL was rather small (6.7–9.6%), suggesting that superior winter hardiness of F. pratensis compared to L. perenne is conferred by multiple small-effect QTLs. We also detected a previously unreported negative effect of Festuca introgression on winter hardiness. Newly obtained QTL information in this study would contribute to the design of Festuca/Lolium hybrid breeding.  相似文献   

10.
Direct seeding of rice as a method of crop establishment is increasingly being adopted by farmers as a means of saving labor and reducing costs. However, the method often results in a poor environment for germination as excessive water levels after seeding can cause poor seedling establishment and a concomitant reduction in yield potential, especially in submergence-prone areas. In this study, we discovered QTLs associated with tolerance of anaerobic germination (AG) in new genetic accessions using genotypic data derived from the Illumina 6K SNP chip. The mapping population developed for QTL analysis comprised 285 F2:3 plants derived from a cross between Tai Nguyen and Anda. In order to evaluate AG tolerance within the mapping population, phenotyping was carried out under anaerobic conditions for 21 days. Three QTLs associated with AG tolerance were identified in the population, qAG1a and qAG1b on chromosome 1 and qAG8 on chromosome 8 using composite interval mapping (CIM). The percentage of variance explained by these QTLs ranged from 5.49 to 14.14%. The lines with three QTLs (qAG1b?+?qAG1a?+?qAG8) demonstrated an approximate 50% survival rate under anaerobic conditions, while lines with two QTLs including qAG1b demonstrated survival rates of 36 and 32% after the treatment, respectively. The QTLs detected in this study may be used to improve AG tolerance during germination and may be combined with other QTLs for anaerobic germination to enhance adaptation to direct seeding and to broaden the understanding of the genetic control of tolerance of germination under anaerobic conditions.  相似文献   

11.
Pseudostems of bunching onion (Allium fistulosum L.) show wide variation in morphological traits and skin color. However, despite being one of the most important agronomic traits, molecular studies of bunching onion pseudostems remain limited. In this study, six morphological traits (plant height, leaf length, pseudostem length, leaf width, pseudostem width and number of leaf sheaths) along with pseudostem pigmentation indices were evaluated in two field trials using an F2:3 population derived from a single F1 cross between a white single pseudostem (non-tillering) and a red tillering bunching onion. Plant height was highly correlated with both leaf length and pseudostem length, but not the number of leaf sheaths. In contrast, the number of leaf sheaths was significantly negatively correlated with both leaf width and pseudostem width. A total of 27 QTLs for the six morphological traits were detected in 16 regions of 11 linkage groups, with a major QTL for the number of leaf sheaths repeatedly detected on Chr. 8. Meanwhile, two QTLs associated with pseudostem pigmentation were repeatedly detected on linkage groups Chr. 4a and Chr. 5a-2. The latter (qPig5a-2) was considered a major QTL, and its location estimated by marker genotyping of the F2 population around the qPig5a-2 region as being within a 7.6 cM interval.  相似文献   

12.
The brown planthopper (BPH) is a potent pest of rice in Asia and Southeast Asia. Host resistance has been found to be the most suitable alternative to manage the insect. But varietal resistance has been found to be short-lived. There has been a constant search for alternate resistance genes. We developed an F8 recombinant inbred population for the BPH resistance gene in Salkathi, an indica landrace from Odisha, India. Phenotyping of RILs against the BPH population at Cuttack, Odisha showed continuous skewed variation with four peaks at 2.1–3.0, 4.1–5.0, 6.1–7.0 and 8.1–9.0 SES score, suggesting the involvement of quantitative loci for resistance to BPH in Salkathi. Mapping showed the presence of two QTLs on the short arm of chromosome 4. One QTL, with phenotype variance of 37.02% is located between the markers RM551 and RM335. The other QTL, with phenotype variance of 7.1% is located between markers RM335 and RM5633. The two QTLs have been designated as qBph4.3 and qBph4.4. QBph4.3 seems to be a novel QTL associated with BPH resistance. We have successfully transferred qBph4.3 and qBph4.4 into two elite rice cultivars, Pusa 44 and Samba Mahsuri. Fine mapping of the identified QTLs may lead to a successful transfer of QTLs into other elite germplasm backgrounds.  相似文献   

13.
Low phosphorus availability is a major factor limiting rice productivity. In this study, a population of backcross recombinant inbred lines (BILs) derived from an inter-specific cross (Oryza sativa L. × O. rufipogon Griff.) was used for genetic linkage map construction and quantitative trait locus (QTL) mapping. The results showed that a linkage map consisting of 153 markers was constructed. Twenty-one out of 231 BILs were tolerant of low-phosphorus according to the index to P-deficiency tolerance. Twenty-three QTLs on chromosomes 1, 2, 3, 7, 8, 9 and 11 were detected, of which eight QTLs showed high (22.93–37.32%) contribution to phenotypic variation. In addition, most of QTLs in this study (18 out of 23 QTLs) were located and overlapped on the chromosome 1, 3 and 11, which individually explained 6.07–34.70% phenotypic variation, indicating that there might be multiple main effect QTLs related to P-deficiency tolerance in O. rufipogon, and these QTLs might cluster in the same region. These results would provide helpful information for cloning and utilizing the P-deficiency tolerance-responsive genes from O. rufipogon.  相似文献   

14.
Wheat (Triticum aestivum L.) yield is directly proportional to physio-morphological traits. A high-density genetic map consisting of 2575 markers was used for mapping QTL controlling stay-green and agronomic traits in wheat grown under four diverse water regimes. A total of 108 additive QTL were identified in target traits. Among them, 28 QTL for chlorophyll content (CC) were detected on 11 chromosomes, 43 for normalized difference vegetation index (NDVI) on all chromosomes except 5B, 5D, and 7D, five for spikes per plant (NSP) on different chromosomes, nine for plant height (PH) on four chromosomes, and 23 for thousand-kernel weight (TKW) on 11 chromosomes. Considering all traits, the phenotypic variation explained (PVE) ranged from 3.61 to 41.62%. A major QTL, QNDVI.cgb-5A.7, for NDVI with a maximum PVE of 20.21%, was located on chromosome 5A. A stable and major PH QTL was observed on chromosome 4D with a PVE close to 40%. Most distances between QTL and corresponding flanking markers were less than 1 cM, and approximately one-third of the QTL coincided with markers. Each of 16 QTL clusters on 10 chromosomes controlled more than one trait and therefore could be regarded as pleiotropic regions in response to different water regimes. Forty-one epistatic QTL were identified for all traits having PVE of 6.00 to 25.07%. Validated QTL closely linked to flanking markers will be beneficial for marker-assisted selection in improving drought-tolerance in wheat.  相似文献   

15.
Both low-temperature germinability (LTG) and cold tolerance at the seedling stage (CTS) are important traits for rice. In this study, a rice population of recombinant inbred lines (RILs), derived from the backcross population of a cross between Dongnong422 and Kongyu131, was developed to detect quantitative trait loci (QTL) affecting LTG and CTS by using seed of different storage times. Correlation analysis indicated that there was no significant relationship between LTG and CTS, suggesting that cold tolerance might be genetic differences for LTG and CTS. In total, Twelve and twenty-three major QTLs were detected for LTG and CTS, respectively, which could explain greater than 10% of the phenotypical variation. Eight (qCG12-1, qGI12-1, qGV9-1, qMLIT12-1, qPV6-1, qMDG12-1, qLDWcold10-1, qLFWcold10-1) significant QTLs were mapped for different storage time, it concluded that such QTLs were not affected by environment (storage time) and were closely related QTLs to cold tolerance. One or more QTLs were identified for each trait with some of these QTLs co-locating, qMLIT7-1, qCG7-1, and qGI7-1 for LTG, qLFWcold10-1, and qLDWcold10-1 for CTS with contributions over 15% were mapped common marker interval, respectively, co-location of QTLs for different traits can be an indication that a locus has pleiotropic effects on multiple traits due to a common mechanistic basis. Two lines, RIL128 and RIL73, might be valuable to improve the LTG and CTS through a combination of crosses. The identified QTLs might be applicable to improve the rice cold tolerance by the marker-assisted selection approach.  相似文献   

16.
The cacao tree (Theobroma cacao L.) is a species of great importance because cacao beans are the raw material used in the production of chocolate. However, the economic success of cacao is largely limited by important diseases such as black pod, which is responsible for losses of up to 30–40% of the global cacao harvest. The discovery of resistance genes could extensively reduce these losses. Therefore, the aims of this study were to construct an integrated multipoint genetic map, align polymorphisms against the available cacao genome, and identify quantitative trait loci (QTLs) associated with resistance to black pod disease in cacao. The genetic map had a total length of 956.41 cM and included 186 simple sequence repeat (SSR) markers distributed among 10 linkage groups. The physical “in silico” map covered more than 200 Mb of the cacao genome. Based on the mixed model predicted means of Phytophthora evaluation, a total of 6 QTLs were detected for Phytophthora palmivora (1 QTL), Phytophthora citrophthora (1 QTL), and Phytophthora capsici (4 QTLs). Approximately 1.77–3.29% of the phenotypic variation could be explained by the mapped QTLs. Several SSR marker-flanking regions containing mapped QTLs were located in proximity to disease regions. The greatest number of resistance genes was detected in linkage group 6, which provides strong evidence for a QTL. This joint analysis involving multipoint and mixed-model approaches may provide a potentially promising technique for detecting genes resistant to black pod and could be very useful for future studies in cacao breeding.  相似文献   

17.
Fusarium wilt (FW; caused by Fusarium oxysporum f. sp. ciceris) and Ascochyta blight (AB; caused by Ascochyta rabiei) are two major biotic stresses that cause significant yield losses in chickpea (Cicer arietinum L.). In order to identify the genomic regions responsible for resistance to FW and AB, 188 recombinant inbred lines derived from a cross JG 62 × ICCV 05530 were phenotyped for reaction to FW and AB under both controlled environment and field conditions. Significant variation in response to FW and AB was detected at all the locations. A genetic map comprising of 111 markers including 84 simple sequence repeats and 27 single nucleotide polymorphism (SNP) loci spanning 261.60 cM was constructed. Five quantitative trait loci (QTLs) were detected for resistance to FW with phenotypic variance explained from 6.63 to 31.55%. Of the five QTLs, three QTLs including a major QTL on CaLG02 and a minor QTL each on CaLG04 and CaLG06 were identified for resistance to race 1 of FW. For race 3, a major QTL each on CaLG02 and CaLG04 were identified. In the case of AB, one QTL for seedling resistance (SR) against ‘Hisar race’ and a minor QTL each for SR and adult plant resistance against isolate 8 of race 6 (3968) were identified. The QTLs and linked markers identified in this study can be utilized for enhancing the FW and AB resistance in elite cultivars using marker-assisted backcrossing.  相似文献   

18.
Two recombinant inbred line F10 rice populations (IAPAR-9/Akihikari and IAPAR-9/Liaoyan241) were used to identify quantitative trait loci (QTLs) for ten drought tolerance traits at the budding and early seedling stage under polyethylene glycol-induced drought stress, and two traits of leaf rolling index (LRI) and leaf withering degree (LWD) under field drought stress. The results showed that the drought-tolerance capacity of IAPAR-9 was stronger than that of Akihikari and Liaoyan241. Thirty-four QTLs for 12 drought tolerance traits were detected, and among them, in the IAPAR-9/Akihikari population, qLRI9-1 and qLRI10-1 for LRI were repeatedly detected in RM3600-RM553 on chromosome 9 and in RM6100-RM3773 on chromosome 10, respectively, at two times points of July 31 and August 13 in 2014. The two QTLs are stable against the environmental impact, and qLRI9-1 and qLRI10-1 explained 6.77–13.66% and 5.01–8.32% of the phenotypic variance, respectively, at the two times points. qLWD9-2 for LWD in the IAPAR-9/Liaoyan241 population contributed 8.73% of variation was detected in the same marker interval with the qLRI9-1, and qLRI1-1 for LRI and qLWD1-1 for LWD were located in the same marker interval RM11054-RM5646 on chromosome 1, which contributed 18.82 and 5.78% of phenotype variation respectively. qGV3 for germination vigor and qRGV3 for relative germination vigor at the budding stage were detected in the same marker interval RM426-RM570 on chromosome 3, which explained 14.98 and 16.30% of the observed phenotypic variation respectively, representing major QTLs. The above-mentioned stable or major QTLs regions could be useful for molecular marker assisted selection breeding, fine mapping, and cloning.  相似文献   

19.
P. Wu  G. Zhang  N. Huang 《Euphytica》1996,89(3):349-354
Summary Segregation of plant height (PH), tiller number (TN), panicle number (PN), average panicle length per plant (PL), average primary branch number per panicle per plant (PBN) and 1000 grain weight (1000G) were specific in an F2 population derived from a cross of Palawan, a tall Javanica variety, and IR42, an Indica semidwarf variety. One hundred and four informative RFLP markers covering all 12 chromosomes were used for detecting putative QTLs controlling the traits. Orthogonal contrasts and interval mapping analysis were used for the analysis. QTL detected for PH on the region of chromosome 1, where semidwarfing gene sd-1 locus is located, seems to be a multiple allelic locus. An additional QTL for PH was identified on chromosome 2. Two QTLs for TN were detected on chromosomes 4 and 12. The QTL on chromosome 4 seemed also to govern the variation in PN. Four QTLs were found for the other traits, two of them for PL were located on chromosomes 6 and 2, one for PBN on chromosome 6 and the other for 1000G on chromosome 1. Additive gene actions were found to be predominant, except one QTL for PH and one QTL for PL, but partial or incomplete dominance also existed for the QTLs detected.  相似文献   

20.
The efficiency of quantitative trait locus (QTL) mapping methods needs to be investigated assuming high single nucleotide polymorphism (SNP) density and low heritability QTLs. This study assessed the efficiency of the least squares, maximum likelihood, and Bayesian approaches for QTL mapping assuming high SNP density and low heritability QTLs. We simulated 50 samples of 400 F2 individuals, which were genotyped for 1000 SNPs (average density of one SNP/centiMorgan) and phenotyped for three traits controlled by 12 QTLs and 88 minor genes. The genes were randomly distributed in the regions covered by the SNPs along ten chromosomes. The QTL heritabilities ranged from approximately 1–2% and the sample sizes were 200 and 400. The power of QTL detection ranged from 30 to 60%, the false discovery rate (FDR) ranged from only 0.5–1.2%, and the bias in the QTL position ranged from 4 to 6 cM. The QTL mapping efficiency was not influenced by the degree of dominance. The statistical approaches were comparable regarding the FDR. Regression-based and simple interval mapping methods showed equivalent power of QTL detection and mapping precision. Compared to interval mapping, the inclusive composite interval mapping provided slightly greater QTL detection power and mapping precision only for the intermediate and high heritability QTLs. By maximizing the prior number of QTLs, the Bayesian analysis provided the greatest power of QTL detection. No method proved to be superior.  相似文献   

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