scholarly journals Mapping of quantitative trait loci for purple stigma and purple apiculus in rice by using a Zhenshan 97B/Minghui 63 RIL population

2021 ◽  
Author(s):  
Jiping Tong ◽  
Zhengshu Han ◽  
Aonan Han
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Indica Rice ◽  
Phenotypic Variance ◽  
Chromosome 6 ◽  
Rice Varieties ◽  
Morphological Marker ◽  
Ril Population ◽  
Trait Loci ◽  
Major Qtl

Anthocyanin pigmentation is an important morphological marker that is commonly used to identify rice varieties and for linkage analysis. The following study investigates the genetic factors involved in the purple stigma (Ps) and purple apiculus (Pa) traits of an important indica rice cross between Zhenshan 97 (purple stigma and purple apiculus) and Minghui 63 (grey stigma and colourless apiculus). A recombinant inbred line (RIL) population derived from this cross was used for quantitative trait loci (QTL) mapping of the purple stigma and purple apiculus traits. As a result, one major QTL for the purple stigma trait, temporarily designated qPS-1-1, and one major QTL for the purple apiculus trait, temporarily designated qPA-1-1, were mapped to the short arm of chromosome 6 in the interval between the two markers Y4073L and *P. The LOD peaks of qPS-1-1 and qPA-1-1 were 44.0127 and 173.3585, respectively. In addition, qPS-1-1 and qPA-1-1 explained 66.7416% and 98.6441% of the total phenotypic variance, respectively. The Zhenshan 97 allele increased the purple stigma trait by approximately 8.0355% (for qPS-1-1) and 9.8863% (for qPA-1-1). Moreover, since qPS-1-1 and qPA-1-1 were strongly correlated, they were also located in the same vicinity of the C gene on the short arm of chromosome 6, which suggested that the two QTL might be the same. By comparing these and previous results, it was deduced that qPS-1-1 or qPA-1-1 was the C gene and was pleiotropic for both the colouration of the apiculus and the colouration of the stigma in rice.

scholarly journals Mapping of Quantitative Trait Loci for Exserted Stigma Rate By Using (ZS97B/MH63) Ril Population

2021 ◽  
Vol 50 (3) ◽  
pp. 551-556
Author(s):  
Jiping Tong ◽  
Zhengshu Han ◽  
Aonan Han
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Seed Set ◽  
Hybrid Rice ◽  
Indica Rice ◽  
Phenotypic Variance ◽  
Total Phenotypic Variance ◽  
Ril Population ◽  
Trait Loci ◽  
Stigma Exsertion

For increasing pollination and seed set, stigma exsertion has been identified as a major component in hybrid rice. By using a recombinant inbred line (RIL) population derived from an important Indica rice cross between Zhenshan97 and Minghui63, a molecular marker-based analysis of quantitative trait loci (QTL) for stigma exsertion was performed. As a result, six prominent QTL were detected for the exserted stigma rate on chromosome 6, 2, 9, 3, 5 and 1, respectively. qSER-1-1, qSER-2-1, qSER-5-1, qSER-6-1, qSER-15-1, and qSER-18-1 explained 8.1515, 4.6657, 7.2387, 4.8997, 6.925 and 6.9291% of the total phenotypic variance, respectively. In addition, for the qSER-1-1 and qSER-2-1, the ZS97B allele increased exserted stigma rate by about 4.3484 and 3.2836%, respectively; while for qSER-5-1, qSER-6-1, qSER-15-1 and qSER-18-1, the MH63 allele increased exserted stigma rate by approx. 4.1527, 3.4243, 3.9801 and 4.0025%, respectively. Bangladesh J. Bot. 50(3): 551-556, 2021 (September)

scholarly journals Genetic Mapping Identifies Consistent Quantitative Trait Loci for Yield Traits of Rice under Greenhouse Drought Conditions

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 62
Author(s):  
Niranjan Baisakh ◽  
Jonalyn Yabes ◽  
Andres Gutierrez ◽  
Venkata Mangu ◽  
Peiyong Ma ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Grain Yield ◽  
Drought Resistance ◽  
Quantitative Trait ◽  
Chromosome 1 ◽  
Phenotypic Variance ◽  
Yield Traits ◽  
Rice Varieties ◽  
Drought Tolerant ◽  
Trait Loci

Improving drought resistance in crops is imperative under the prevailing erratic rainfall patterns. Drought affects the growth and yield of most modern rice varieties. Recent breeding efforts aim to incorporate drought resistance traits in rice varieties that can be suitable under alternative irrigation schemes, such as in a (semi)aerobic system, as row (furrow-irrigated) rice. The identification of quantitative trait loci (QTLs) controlling grain yield, the most important trait with high selection efficiency, can lead to the identification of markers to facilitate marker-assisted breeding of drought-resistant rice. Here, we report grain yield QTLs under greenhouse drought using an F2:3 population derived from Cocodrie (drought sensitive) × Nagina 22 (N22) (drought tolerant). Eight QTLs were identified for yield traits under drought. Grain yield QTL under drought on chromosome 1 (phenotypic variance explained (PVE) = 11.15%) co-localized with the only QTL for panicle number (PVE = 37.7%). The drought-tolerant parent N22 contributed the favorable alleles for all QTLs except qGN3.2 and qGN5.1 for grain number per panicle. Stress-responsive transcription factors, such as ethylene response factor, WD40 domain protein, zinc finger protein, and genes involved in lipid/sugar metabolism were linked to the QTLs, suggesting their possible role in drought tolerance mechanism of N22 in the background of Cocodrie, contributing to higher yield under drought.

Identification of microsatellite markers linked to quantitative trait loci controlling resistance to Fusarium root rot in field pea

2011 ◽  
Vol 91 (1) ◽  
pp. 199-204 ◽  
Author(s):  
J. Feng ◽  
R. Hwang ◽  
K. F. Chang ◽  
R. L. Conner ◽  
S. F. Hwang ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Microsatellite Markers ◽  
Quantitative Trait ◽  
Root Rot ◽  
Field Experiments ◽  
Field Pea ◽  
Phenotypic Variance ◽  
Fusarium Root Rot ◽  
Ril Population ◽  
Trait Loci

Feng, J., Hwang, R., Chang, K. F., Conner, R. L., Hwang, S. F., Strelkov, S. E., Gossen, B. D., McLaren, D. L. and Xue, A. G. 2011. Identification of microsatellite markers linked to quantitative trait loci controlling resistance to Fusarium root rot in field pea. Can. J. Plant Sci. 91: 199–204. Fusarium root rot, caused by Fusarium solani (Mart.) Sacc. f. sp. pisi (F. R. Jones) W. C. Snyder & H. N. Hans, is the most common root disease of field pea (Pisum sativum L.) in western Canada. In this study, a recombinant inbred line (RIL) population (n=71) of field pea, derived from crosses between a resistant cultivar Carman, and a susceptible cultivar Reward, was evaluated to identify quantitative trait loci (QTL) controlling resistance to Fusarium root rot. The parental genotypes and RILs were evaluated for resistance to root rot following inoculation with F. solani in field experiments during 2007 and 2008. The frequency distribution of disease severities among the RILs was continuous. Transgressive segregation for resistance was observed among the RILs, with five lines more resistant than Carman, but no lines were more susceptible than Reward. To identify DNA markers linked with the resistance, 213 microsatellite markers were screened with genomic DNA from the two parental cultivars. Only 14 markers were polymorphic between the two parents and were used to genotype each of the RILs. Quantitative trait loci analysis based on the mean disease severity data from 2007 and 2008 identified a QTL that explained 39.0% of the phenotypic variance in the RIL population. This QTL is flanked by markers AA416 and AB60 on linkage group VII. The microsatellite markers that are closely linked to this QTL may be useful for marker assisted selection to develop cultivars with superior Fusarium root rot resistance.

scholarly journals Conditional Mapping Identified Quantitative Trait Loci for Grain Protein Concentration Expressing Independently of Grain Yield in Canadian Durum Wheat

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuefeng Ruan ◽  
Bianyun Yu ◽  
Ron E. Knox ◽  
Wentao Zhang ◽  
Asheesh K. Singh ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Grain Yield ◽  
Durum Wheat ◽  
Quantitative Trait ◽  
Protein Concentration ◽  
Grain Protein ◽  
Phenotypic Variance ◽  
Grain Protein Concentration ◽  
Trait Loci ◽  
Major Qtl

Grain protein concentration (GPC) is an important trait in durum cultivar development as a major determinant of the nutritional value of grain and end-use product quality. However, it is challenging to simultaneously select both GPC and grain yield (GY) due to the negative correlation between them. To characterize quantitative trait loci (QTL) for GPC and understand the genetic relationship between GPC and GY in Canadian durum wheat, we performed both traditional and conditional QTL mapping using a doubled haploid (DH) population of 162 lines derived from Pelissier × Strongfield. The population was grown in the field over 5 years and GPC was measured. QTL contributing to GPC were detected on chromosome 1B, 2B, 3A, 5B, 7A, and 7B using traditional mapping. One major QTL on 3A (QGpc.spa-3A.3) was consistently detected over 3 years accounting for 9.4–18.1% of the phenotypic variance, with the favorable allele derived from Pelissier. Another major QTL on 7A (QGpc.spa-7A) detected in 3 years explained 6.9–14.8% of the phenotypic variance, with the beneficial allele derived from Strongfield. Comparison of the QTL described here with the results previously reported led to the identification of one novel major QTL on 3A (QGpc.spa-3A.3) and five novel minor QTL on 1B, 2B and 3A. Four QTL were common between traditional and conditional mapping, with QGpc.spa-3A.3 and QGpc.spa-7A detected in multiple environments. The QTL identified by conditional mapping were independent or partially independent of GY, making them of great importance for development of high GPC and high yielding durum.

Quantitative Trait Loci for Susceptibility to Tapeworm Infection in the Red Flour Beetle

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1307-1315
Author(s):  
Daibin Zhong ◽  
Aditi Pai ◽  
Guiyun Yan
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Genetic Basis ◽  
Life Cycles ◽  
Red Flour Beetle ◽  
Phenotypic Variance ◽  
Flour Beetle ◽  
Trait Loci ◽  
Host Ecology ◽  
Tapeworm Infection

Abstract Parasites have profound effects on host ecology and evolution, and the effects of parasites on host ecology are often influenced by the magnitude of host susceptibility to parasites. Many parasites have complex life cycles that require intermediate hosts for their transmission, but little is known about the genetic basis of the intermediate host's susceptibility to these parasites. This study examined the genetic basis of susceptibility to a tapeworm (Hymenolepis diminuta) in the red flour beetle (Tribolium castaneum) that serves as an intermediate host in its transmission. Quantitative trait loci (QTL) mapping experiments were conducted with two independent segregating populations using amplified fragment length polymorphism (AFLP) markers and randomly amplified polymorphic DNA (RAPD) markers. A total of five QTL that significantly affected beetle susceptibility were identified in the two reciprocal crosses. Two common QTL on linkage groups 3 and 6 were identified in both crosses with similar effects on the phenotype, and three QTL were unique to each cross. In one cross, the three main QTL accounted for 29% of the total phenotypic variance and digenic epistasis explained 39% of the variance. In the second cross, the four main QTL explained 62% of the variance and digenic epistasis accounted for only 5% of the variance. The actions of these QTL were either overdominance or underdominance. Our results suggest that the polygenic nature of beetle susceptibility to the parasites and epistasis are important genetic mechanisms for the maintenance of variation within or among beetle strains in susceptibility to tapeworm infection.

scholarly journals The Genetic Basis of the Interspecific Differences in Wing Size in Nasonia (Hymenoptera; Pteromalidae): Major Quantitative Trait Loci and Epistasis

Genetics ◽  
2002 ◽  
Vol 161 (2) ◽  
pp. 673-684
Author(s):  
J Gadau ◽  
R E Page ◽  
J H Werren
Keyword(s):  
Quantitative Trait Loci ◽  
Qtl Analysis ◽  
Quantitative Trait ◽  
Wing Length ◽  
Size Difference ◽  
Phenotypic Variance ◽  
Wing Size ◽  
Epistatic Interactions ◽  
Trait Loci ◽  
Wing Width

Abstract There is a 2.5-fold difference in male wing size between two haplodiploid insect species, Nasonia vitripennis and N. giraulti. The haploidy of males facilitated a full genomic screen for quantitative trait loci (QTL) affecting wing size and the detection of epistatic interactions. A QTL analysis of the interspecific wing-size difference revealed QTL with major effects and epistatic interactions among loci affecting the trait. We analyzed 178 hybrid males and initially found two major QTL for wing length, one for wing width, three for a normalized wing-size variable, and five for wing seta density. One QTL for wing width explains 38.1% of the phenotypic variance, and the same QTL explains 22% of the phenotypic variance in normalized wing size. This corresponds to a region previously introgressed from N. giraulti into N. vitripennis that accounts for 44% of the normalized wing-size difference between the species. Significant epistatic interactions were also found that affect wing size and density of setae on the wing. Screening for pairwise epistatic interactions between loci on different linkage groups revealed four additional loci for wing length and four loci for normalized wing size that were not detected in the original QTL analysis. We propose that the evolution of smaller wings in N. vitripennis males is primarily the result of major mutations at few genomic regions and involves epistatic interactions among some loci.

Quantitative Trait Loci Affecting Differences in Floral Morphology Between Two Species of Monkeyflower (Mimulus)

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 367-382 ◽  
Author(s):  
H D Bradshaw ◽  
Kevin G Otto ◽  
Barbara E Frewen ◽  
John K McKay ◽  
Douglas W Schemske
Keyword(s):  
Quantitative Trait Loci ◽  
Reproductive Isolation ◽  
Quantitative Trait ◽  
Floral Morphology ◽  
Cumulative Effect ◽  
Sympatric Species ◽  
Accurate Estimate ◽  
Phenotypic Variance ◽  
Trait Loci ◽  
Morphological Differences

Abstract Conspicuous differences in floral morphology are partly responsible for reproductive isolation between two sympatric species of monkeyflower because of their effect on visitation of the flowers by different pollinators. Mimulus lewisii flowers are visited primarily by bumblebees, whereas M. cardinalis flowers are visited mostly by hummingbirds. The genetic control of 12 morphological differences between the flowers of M. lewisii and M. cardinalis was explored in a large linkage mapping population of F2 plants (n = 465) to provide an accurate estimate of the number and magnitude of effect of quantitative trait loci (QTLs) governing each character. Between one and six QTLs were identified for each trait. Most (9/12) traits appear to be controlled in part by at least one major QTL explaining ≥25% of the total phenotypic variance. This implies that either single genes of individually large effect or linked clusters of genes with a large cumulative effect can play a role in the evolution of reproductive isolation and speciation.

scholarly journals Quantitative Trait Loci Affecting Survival and Fertility-Related Traits in Caenorhabditis elegans Show Genotype-Environment Interactions, Pleiotropy and Epistasis

Genetics ◽  
1999 ◽  
Vol 153 (3) ◽  
pp. 1233-1243 ◽  
Author(s):  
David R Shook ◽  
Thomas E Johnson
Keyword(s):  
Caenorhabditis Elegans ◽  
Quantitative Trait Loci ◽  
Population Growth ◽  
Quantitative Trait ◽  
Age Of Onset ◽  
Inbred Strains ◽  
Interval Mapping ◽  
Phenotypic Variance ◽  
Epistatic Interactions ◽  
Trait Loci

Abstract We have identified, using composite interval mapping, quantitative trait loci (QTL) affecting a variety of life history traits (LHTs) in the nematode Caenorhabditis elegans. Using recombinant inbred strains assayed on the surface of agar plates, we found QTL for survival, early fertility, age of onset of sexual maturity, and population growth rate. There was no overall correlation between survival on solid media and previous measures of survival in liquid media. Of the four survival QTL found in these two environments, two have genotype-environment interactions (GEIs). Epistatic interactions between markers were detected for four traits. A multiple regression approach was used to determine which single markers and epistatic interactions best explained the phenotypic variance for each trait. The amount of phenotypic variance accounted for by genetic effects ranged from 13% (for internal hatching) to 46% (for population growth). Epistatic effects accounted for 9–11% of the phenotypic variance for three traits. Two regions containing QTL that affected more than one fertility-related trait were found. This study serves as an example of the power of QTL mapping for dissecting the genetic architecture of a suite of LHTs and indicates the potential importance of environment and GEIs in the evolution of this architecture.

Quantitative Trait Loci for Yield Traits Located Between Hd3a and Hd1 on Short Arm of Chromosome 6 in Rice

Rice Science ◽  
2011 ◽  
Vol 18 (4) ◽  
pp. 257-264 ◽  
Author(s):  
Ye-yang FAN ◽  
Chen CHEN ◽  
Ji-rong WU ◽  
Shi-hua CHENG ◽  
Jie-yun ZHUANG
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Chromosome 6 ◽  
Yield Traits ◽  
Trait Loci

scholarly journals Meta-Analysis of Quantitative Trait Loci Associated with Seedling-Stage Salt Tolerance in Rice (Oryza sativa L.)

Plants ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 33 ◽  
Author(s):  
Md. Islam ◽  
John Ontoy ◽  
Prasanta Subudhi
Keyword(s):  
Quantitative Trait Loci ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Oryza Sativa L ◽  
Meta Analysis ◽  
Seedling Stage ◽  
Phenotypic Variance ◽  
A Genome ◽  
Trait Loci

Soil and water salinity is one of the major abiotic stresses that reduce growth and productivity in major food crops including rice. The lack of congruence of salt tolerance quantitative trait loci (QTLs) in multiple genetic backgrounds and multiple environments is a major hindrance for undertaking marker-assisted selection (MAS). A genome-wide meta-analysis of QTLs controlling seedling-stage salt tolerance was conducted in rice using QTL information from 12 studies. Using a consensus map, 11 meta-QTLs for three traits with smaller confidence intervals were localized on chromosomes 1 and 2. The phenotypic variance of 3 meta-QTLs was ≥20%. Based on phenotyping of 56 diverse genotypes and breeding lines, six salt-tolerant genotypes (Bharathy, I Kung Ban 4-2 Mutant, Langmanbi, Fatehpur 3, CT-329, and IARI 5823) were identified. The perusal of the meta-QTL regions revealed several candidate genes associated with salt-tolerance attributes. The lack of association between meta-QTL linked markers and the level of salt tolerance could be due to the low resolution of meta-QTL regions and the genetic complexity of salt tolerance. The meta-QTLs identified in this study will be useful not only for MAS and pyramiding, but will also accelerate the fine mapping and cloning of candidate genes associated with salt-tolerance mechanisms in rice.

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