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.

Molecular mapping of quantitative trait loci for kernel morphology traits in a non-1BL.1RS×1BL.1RS wheat cross

2011 ◽  
Vol 62 (8) ◽  
pp. 625 ◽  
Author(s):  
Yonggui Xiao ◽  
Shengmei He ◽  
Jun Yan ◽  
Yong Zhang ◽  
Yelun Zhang ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Grain Yield ◽  
Quantitative Trait ◽  
Molecular Mapping ◽  
Length Ratio ◽  
Phenotypic Variance ◽  
Kernel Length ◽  
Main Effect ◽  
Trait Loci ◽  
Kernel Morphology

The improvement of kernel morphology traits is an important goal in common wheat (Triticum aestivum L.) breeding programs because of their close relationship with grain yield and milling quality. The aim of this study was to map quantitative trait loci (QTL) for kernel morphology traits using 240 recombinant inbred lines derived from a cross between the non-1BL.1RS translocation cv. PH 82-2 and the 1BL.1RS translocation cv. Neixiang 188, grown in six environments in China. Inclusive composite interval mapping identified 71 main-effect QTL on 16 chromosomes for seven kernel morphology traits measured by digital imaging, viz. kernel length, width, perimeter, area, shape factor, factor form-density and width/length ratio. Each of these loci explained from 2.6 to 28.2% of the phenotypic variation. Eight QTL clusters conferring the largest effects on kernel weight and kernel morphology traits were detected on chromosomes 1BL.1RS (2), 2A, 4A, 4B, 6B, 6D and 7A. Fourteen epistatic QTL were identified for all kernel morphology traits except kernel width/length ratio, involving 24 main-effect QTL distributed on 13 chromosomes, and explaining 2.5–8.3% of the phenotypic variance. Five loci, viz. Sec-1 on 1BL.1RS, Glu-B1 on 1BL, Xcfe53 on 2A, Xwmc238 on 4B, and Xbarc174 on 7A, were detected consistently across environments, and their linked DNA markers may be used for marker-assisted selection in breeding for improved wheat kernel traits and grain yield.

Dynamic quantitative trait loci for salt stress components on chromosome 1 of rice

2010 ◽  
Vol 37 (7) ◽  
pp. 634 ◽  
Author(s):  
Tanveer Ul Haq ◽  
John Gorham ◽  
Javaid Akhtar ◽  
Nasim Akhtar ◽  
Katherine A. Steele
Keyword(s):  
Salt Stress ◽  
Quantitative Trait Loci ◽  
Linkage Map ◽  
Quantitative Trait ◽  
Recombinant Inbred Lines ◽  
Leaf Age ◽  
Chromosome 1 ◽  
Rflp Markers ◽  
Rice Varieties ◽  
Trait Loci

Rice varieties Co39 and Moroberekan differ for leaf Na+ concentrations when grown at moderate salinity (100–150 mol m–3 NaCl; 10 : 1 or 20 : 1 Na+ to Ca2+ ratio). Recombinant inbred lines (RILs) from a cross between them were used to map quantitative trait loci (QTL) under salt stress over several weeks. Two experiments (conducted with 170 and 96 RILs, and a linkage map of 126 RFLP markers) identified a major effect on QTL for leaf Na+ concentration and K+ : Na+ ratio on chromosome 1 in a region corresponding to 11.07–14.6 Mbp. No leaf Cl– QTL were detected. In a third experiment, leaves and sheaths were harvested after 7 and 21 days at 100 mol m–3 NaCl. The linkage map of chromosome 1 was improved by the addition of 28 microsatellite markers, which resolved distinct QTL for Na+ and K+ concentrations, and K+ : Na+ ratio. After 7 days’ stress, the most significant QTL were in the region of 11.56–12.66 Mbp. The highest Na+ concentrations were recorded in the sheaths. Na+ concentration QTL were detected for leaves, but not for sheaths. After 21 days’ stress, the region containing the most significant QTL extended to 11.07 Mbp in leaves and in sheaths. A QTL for the ratio of leaf Na+ to sheath Na+ concentrations was found at 11.39–12.39 Mbp. These findings suggest that multiple genes in this region are involved in the response to salinity, and their impact is dynamic according to stress duration, and leaf age and type.

scholarly journals Substitution mapping of the major quantitative trait loci controlling stigma exsertion rate from Oryza glumaepatula

2020 ◽  
Author(s):  
Quanya Tan ◽  
Tuo Zou ◽  
Mingmin Zheng ◽  
Yuerong Ni ◽  
Xin Luan ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Chromosome 1 ◽  
Rice Seed ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Substitution Mapping ◽  
Trait Loci ◽  
Stigma Exsertion ◽  
Stigma Exsertion Rate

Abstract Background: Stigma exsertion rate (SER) is a key determinant for outcrossing ability of male sterility lines (MSLs) in hybrid rice seed production. Outcrossing ability in cultivated rice varieties has diminished during the process of domestication, while wild Oryza species keep strong outcrossing ability. Here, we detected the quantitative trait loci (QTLs) controlling SER using a set of single-segment substitution lines (SSSLs) derived from O. glumaepatula, a wild Oryza species.Results: Seven QTLs for SER, qSER-1a, qSER-1b, qSER-3a, qSER-3b, qSER-5, qSER-9 and qSER-10, were located on 5 chromosomes. qSER-1a and qSER-1b were located on chromosome 1. qSER-3a and qSER-3b were mapped on chromosome 3, and qSER-3b was further located at an interval of 931.0kb by secondary substitution mapping. qSER-5, qSER-9 and qSER-10 were identified on chromosomes 5, 9 and 10, respectively, and qSER-9 was delimited to a region of 608.2kb by secondary substitution mapping. The additive effects of the 7 QTLs ranged from 10.6% to 14.8%, and the additive contribution variances explained by each of the QTLs were from 36.3% to 50.6%, which were higher than those of most loci for SER reported previously.Conclusions: qSER-1a and qSER-1b were novel loci for SER on chromosome 1. All of the 7 QTLs had major effects on SER. The major QTLs of SER will help to develop MSLs with strong outcrossing ability.

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 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.

scholarly journals Identification and Mapping of Quantitative Trait Loci Conditioning Resistance to Southern Leaf Blight of Maize Caused by Cochliobolus heterostrophus Race O

2004 ◽  
Vol 94 (8) ◽  
pp. 862-867 ◽  
Author(s):  
M. L. Carson ◽  
C. W. Stuber ◽  
M. L. Senior
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Leaf Blight ◽  
Chromosome 1 ◽  
Cochliobolus Heterostrophus ◽  
Phenotypic Variance ◽  
Polygenic Inheritance ◽  
Trait Loci ◽  
Southern Leaf Blight ◽  
Ri Lines

A random set of recombinant inbred (RI) lines (F2:7) derived from the cross of the inbred lines Mo17 (resistant) and B73 (susceptible) were evaluated for resistance to southern leaf blight (SLB) caused by Cochliobolus heterostrophus race O. The RI lines were genotyped at a total of 234 simple sequence repeat, restriction fragment length polymorphism, or isozyme loci. Field plots of the RI lines were inoculated artificially with an aggressive isolate of C. heterostrophus race O in each of two growing seasons in North Carolina. Lines were rated for percent SLB severity two (1996) or three (1995) times during the grain-filling period. Data also were converted to area under the disease progress curve (AUDPC) and analyzed using the composite interval mapping option of the PLABQTL program. When means of disease ratings over years were fitted to models, a total of 11 quantitative trait loci (QTLs) were found to condition resistance to SLB, depending upon which disease ratings were used in the analyses. When the AUDPC data were combined and analyzed over environments, seven QTLs, on chromosomes 1, 2, 3, 4, 7, and 10 were found to come from the resistant parent Mo17. An additional QTL for resistance on chromosome 1 came from the susceptible parent B73. The eight identified QTLs accounted for 46% of the phenotypic variation for resistance. QTL × environment interactions often were highly significant but, with one exception, were the result of differences in the magnitude of QTL effects between years and not due to changes in direction of effects. QTLs on the long arm of chromosome 1 and chromosomes 2 and 3 had the largest effects, were the most consistently detected, and accounted for most of the phenotypic variance. No significant additive × additive epistatic effects were detected. These data support earlier reports of the polygenic inheritance of resistance to SLB of maize.

Quantitative trait loci underlying hatching weight and growth traits in an F2 intercross between two strains of Japanese quail

2012 ◽  
Vol 52 (11) ◽  
pp. 1012 ◽  
Author(s):  
S. S. Sohrabi ◽  
A. K. Esmailizadeh ◽  
A. Baghizadeh ◽  
H. Moradian ◽  
M. R. Mohammadabadi ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Japanese Quail ◽  
Quantitative Trait ◽  
Growth Traits ◽  
Interval Mapping ◽  
Chromosome 1 ◽  
Phenotypic Variance ◽  
Cross Model ◽  
Trait Loci ◽  
Qtl Effects

A three-generation resource population was developed using two distinct Japanese quail strains, wild and white, to map quantitative trait loci underlying hatching weight and growth traits. Eight pairs of white and wild birds were crossed reciprocally and 34 F1 birds were produced. The F1 birds were intercrossed to generate 422 F2 offspring. All of the animals from three generations (472 birds) were genotyped for eight microsatellite markers on chromosome 1. Liveweight data from hatch to 5 weeks of age were collected on the F2 birds. Quantitative trait loci (QTL) analysis was conducted applying the line-cross model and the least-squares interval mapping approach. The results indicated QTL affecting hatching weight and several growth related traits on chromosome 1. The F2 phenotypic variance explained by the detected additive QTL effects ranged from 1.0 to 3.7 for different traits. Modelling both additive and dominance QTL effects revealed additional QTL with significant dominance mode of action affecting pre-slaughter weight. However, there was no evidence for imprinting (parent-of-origin) effects. The variance due to the reciprocal cross effect ranged between 3.0 and 19.1% for weight at 1 week of age and hatching weight, respectively.

scholarly journals Identification of Quantitative Trait Loci Influencing Traits Related to Energy Balance in Selection and Inbred Lines of Mice

Genetics ◽  
1999 ◽  
Vol 152 (2) ◽  
pp. 699-711 ◽  
Author(s):  
D E Moody ◽  
D Pomp ◽  
M K Nielsen ◽  
L D Van Vleck
Keyword(s):  
Quantitative Trait Loci ◽  
Energy Balance ◽  
Heat Loss ◽  
Quantitative Trait ◽  
Subcutaneous Fat ◽  
High Heat ◽  
Chromosome 1 ◽  
Direct Calorimetry ◽  
Resource Population ◽  
Trait Loci

Abstract Energy balance is a complex trait with relevance to the study of human obesity and maintenance energy requirements of livestock. The objective of this study was to identify, using unique mouse models, quantitative trait loci (QTL) influencing traits that contribute to variation in energy balance. Two F2 resource populations were created from lines of mice differing in heat loss measured by direct calorimetry as an indicator of energy expenditure. The HB F2 resource population originated from a cross between a noninbred line selected for high heat loss and an inbred line with low heat loss. Evidence for significant QTL influencing heat loss was found on chromosomes 1, 2, 3, and 7. Significant QTL influencing body weight and percentage gonadal fat, brown fat, liver, and heart were also identified. The LH F2 resource population originated from noninbred lines of mice that had undergone divergent selection for heat loss. Chromosomes 1 and 3 were evaluated. The QTL for heat loss identified on chromosome 1 in the HB population was confirmed in the LH population, although the effect was smaller. The presence of a QTL influencing 6-wk weight was also confirmed. Suggestive evidence for additional QTL influencing heat loss, percentage subcutaneous fat, and percentage heart was found for chromosome 1.

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.

Sign in / Sign up

Export Citation Format

Share Document