scholarly journals QTL analysis in multiple sorghum mapping populations facilitates dissection of the genetic control of agronomic and yield-related traits in sorghum [Sorghum bicolor (Moench)]

2021 ◽  
Author(s):  
Techale Birhan Mekonnen ◽  
Hongxu Dong ◽  
Mihrete Getinet ◽  
Aregash Gabizew ◽  
Andrew Paterson ◽  
...  
Keyword(s):  
Moisture Stress ◽  
Interval Mapping ◽  
Consensus Map ◽  
Allele Distribution ◽  
Lattice Design ◽  
Multiple Loci ◽  
Standing Variation ◽  
Genomic Landscape ◽  
Common Genetic Variants ◽  
Mapping Populations

Abstract The genetic architectures of agronomic and yield-related traits are expected to involve multiple loci that are unlikely all to segregate for alternative alleles in a single bi-parental population. Therefore, the identification of quantitative trait loci (QTL) that are expressed in diverse genetic backgrounds of multiple bi-parental populations provides evidence about both background-specific and common genetic variants. The purpose of this study was to map QTLs for agronomic and yield related traits using three connected mapping populations of different genetic backgrounds, to gain insight into the genomic landscape of these important traits in elite Ethiopian sorghum germplasm. The three bi-parental populations, each with 207 F 2:3 lines were evaluated using an alpha lattice design with two replications under two moisture stress environments. Data analysis was done separately for each population using composite interval mapping, finding a total of 105 QTLs. All the QTLs identified from individual populations were projected on a combined consensus map, comprising a total of 25 meta QTLs for seven traits. The consensus map allowed us to deduce locations of a larger number of markers than possible in any individual map, providing a reference for genetic studies in different genetic backgrounds. The meta QTLs identified in this study could be used for marker-assisted breeding programs in sorghum after validation. Only one trait reduced leaf senescence, showed a striking bias of allele distribution, indicating substantial standing variation among the lines that might be employed in improving drought tolerance of sorghum.

scholarly journals Mapping of Quantitative Trait Loci Controlling Adaptive Traits in Coastal Douglas Fir. III. Quantitative Trait Loci-by-Environment Interactions

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1489-1506
Author(s):  
Kathleen D Jermstad ◽  
Daniel L Bassoni ◽  
Keith S Jech ◽  
Gary A Ritchie ◽  
Nicholas C Wheeler ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Complex Traits ◽  
Moisture Stress ◽  
Interval Mapping ◽  
Douglas Fir ◽  
Adaptive Traits ◽  
Growth Cessation ◽  
Trait Loci ◽  
Growth Initiation

Abstract Quantitative trait loci (QTL) were mapped in the woody perennial Douglas fir (Pseudotsuga menziesii var. menziesii [Mirb.] Franco) for complex traits controlling the timing of growth initiation and growth cessation. QTL were estimated under controlled environmental conditions to identify QTL interactions with photoperiod, moisture stress, winter chilling, and spring temperatures. A three-generation mapping population of 460 cloned progeny was used for genetic mapping and phenotypic evaluations. An all-marker interval mapping method was used for scanning the genome for the presence of QTL and single-factor ANOVA was used for estimating QTL-by-environment interactions. A modest number of QTL were detected per trait, with individual QTL explaining up to 9.5% of the phenotypic variation. Two QTL-by-treatment interactions were found for growth initiation, whereas several QTL-by-treatment interactions were detected among growth cessation traits. This is the first report of QTL interactions with specific environmental signals in forest trees and will assist in the identification of candidate genes controlling these important adaptive traits in perennial plants.

scholarly journals Quantitative Trait Loci for Resistance to Potato Dry Rot Caused by Fusarium sambucinum

Agronomy ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 203
Author(s):  
Sylwester Sobkowiak ◽  
Marta Janiszewska ◽  
Emil Stefańczyk ◽  
Iwona Wasilewicz-Flis ◽  
Jadwiga Śliwka
Keyword(s):  
Interval Mapping ◽  
Potato Cultivars ◽  
Genetic Maps ◽  
Dry Rot ◽  
Potato Genome ◽  
Polygenic Control ◽  
Efficient Breeding ◽  
Chromosome I ◽  
Mapping Populations ◽  
Important Disease

Tuber dry rot is an important disease of potato caused by soil and seed-borne pathogens of the Fusarium genus leading to losses that may reach 60% of the yield. The goal of this work was to study the inheritance of the dry rot resistance in two diploid potato hybrid populations (11-36 and 12-3) with complex pedigrees, including several wild Solanum spp. We used an aggressive isolate of F. sambucinum for phenotyping both progenies, parents, and standard potato cultivars in laboratory tuber tests, in three subsequent years. The QTL for dry rot resistance were mapped by interval mapping on existing genetic maps of both mapping populations. The most important and reproducible QTL for this trait was mapped on chromosome I and additional year- and population-specific QTL were mapped on chromosomes II, VII, IX, XI, and XII, confirming polygenic control of this resistance. This is the first study mapping the loci affecting tuber dry rot resistance in potato genome that can contribute to better understanding of potato-F. sambucinum interaction and to more efficient breeding of resistant potato cultivars.

scholarly journals Mapping QTL for Grain Yield under Moisture Stress Environments in Rice (Oryza sativa L.)

2011 ◽  
Vol 3 (4) ◽  
pp. 129-133
Author(s):  
Supriyo CHAKRABORTY ◽  
Sheng-Chu WANG ◽  
Zhao-Bang ZENG
Keyword(s):  
Grain Yield ◽  
Genetic Variance ◽  
Oryza Sativa L ◽  
Moisture Stress ◽  
Interval Mapping ◽  
Chromosome 1 ◽  
Phenotypic Variance ◽  
Common Qtl ◽  
Rice Chromosomes ◽  
Stress Environments

Polygenes (QTLs) for grain yield were mapped on rice chromosomes under two moisture stress environments by multiple interval mapping (MIM) method in a double haploid (DH) population derived from a cross between a deep-rooted japonica and a shallow-rooted indica genotype. In environment 1 (E1), the MIM detected a total of six QTLs for grain yield on chromosomes-two QTLs on chromosome 1 and four QTLs on chromosome 5 along with one additive x additive epistasis. But in environment 2 (E2), the MIM detected five QTLs for grain yield on two chromosomes-three QTLs on chromosome 1 and two QTLs on chromosome 7. One common QTL on chromosome 1 flanked by the markers RG109-ME1014 was detected in both the environments, although the other detected QTLs differed between environments. The magnitude of QTL effect, percent genetic variance and percent phenotypic variance explained by each QTL was also estimated in both environments. The common QTL explained about 26.05 and 13.93% of genetic variance in E1 and E2, respectively. Estimated broad sense heritability for grain yield was 48.01 in E1 and 25.27% in E2.

scholarly journals Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut

2013 ◽  
Vol 40 (2) ◽  
pp. 95-106 ◽  
Author(s):  
Baozhu Guo ◽  
Manish K. Pandey ◽  
Guohao He ◽  
Xinyou Zhang ◽  
Boshou Liao ◽  
...  
Keyword(s):  
Genetic Linkage ◽  
High Density ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Consensus Map ◽  
Genetic Linkage Maps ◽  
Marker Loci ◽  
Cultivated Peanut ◽  
Peanut Genome ◽  
Mapping Populations

ABSTRACT The competitiveness of peanuts in domestic and global markets has been threatened by losses in productivity and quality that are attributed to diseases, pests, environmental stresses and allergy or food safety issues. Narrow genetic diversity and a deficiency of polymorphic DNA markers severely hindered construction of dense genetic maps and quantitative trait loci (QTL) mapping in order to deploy linked markers in marker-assisted peanut improvement. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to a global effort in 2006 to address these issues through coordination of international efforts in genome research beginning with molecular marker development and improvement of map resolution and coverage. Ultimately, a peanut genome sequencing project was launched in 2012 by the Peanut Genome Consortium (PGC). We reviewed the progress for accelerated development of peanut genomic resources in peanut, such as generation of expressed sequenced tags (ESTs) (252,832 ESTs as December 2012 in the public NCBI EST database), development of molecular markers (over 15,518 SSRs), and construction of peanut genetic linkage maps, in particular for cultivated peanut. Several consensus genetic maps have been constructed, and there are examples of recent international efforts to develop high density maps. An international reference consensus genetic map was developed recently with 897 marker loci based on 11 published mapping populations. Furthermore, a high-density integrated consensus map of cultivated peanut and wild diploid relatives also has been developed, which was enriched further with 3693 marker loci on a single map by adding information from five new genetic mapping populations to the published reference consensus map.

A consensus map of rye integrating mapping data from five mapping populations

2008 ◽  
Vol 118 (4) ◽  
pp. 793-800 ◽  
Author(s):  
J. Perry Gustafson ◽  
Xue-Feng Ma ◽  
Viktor Korzun ◽  
John W. Snape
Keyword(s):  
Consensus Map ◽  
Mapping Data ◽  
Mapping Populations

scholarly journals We shall meet again - Genomics of historical admixture in the sea

2020 ◽  
Author(s):  
Xueyun Feng ◽  
Juha Merilä ◽  
Ari Löytynoja
Keyword(s):  
Local Adaptation ◽  
Source Population ◽  
Genetic Introgression ◽  
Genome Data ◽  
The North ◽  
Standing Variation ◽  
Genomic Landscape ◽  
The North Sea ◽  
Phylogenetic Affinities ◽  
The Impact

AbstractWe studied the impact of genetic introgression in evolution and on evolutionary studies with whole-genome data from two divergent lineages of sticklebacks. Our results reveal that the hybrid zone between the lineages ranges across the entire Baltic Sea and parts of the North Sea with the foreign ancestry decreasing with increasing distance to the source population. Introgression has also penetrated currently isolated freshwater populations. We identified footprints of selection on regions enriched for introgressed variants, suggesting that some of the introgression has been adaptive. However, the levels of introgression were in general negatively correlated with the recombination rate, suggesting that the introgression has been largely neutral and adaptive ancestral standing variation likely had a more important role in shaping the genomic landscape. Our results further suggest that overlooked introgression can mislead analyses of local adaptation and phylogenetic affinities, highlighting the importance of accounting for introgression in studies of local adaptation.

scholarly journals Genetic analysis of grain yield and yield-attributing traits in navy bean (Phaseolus vulgaris L.) under drought and optimal environments

2021 ◽  
Author(s):  
Bruce Mutari ◽  
Julia Sibiya ◽  
Edmore Gasura ◽  
Prince Muchapondwa Matova ◽  
Kennedy Simango ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Grain Yield ◽  
Combining Ability ◽  
Moisture Stress ◽  
Square Lattice ◽  
Navy Bean ◽  
Gene Effects ◽  
Positive Effects ◽  
Lattice Design ◽  
Diallel Mating Design

Abstract Knowledge of the genetic basis of navy bean (Phaseolus vulgaris L.) performance under drought stress (DS) is important for planning appropriate breeding and selection strategies in DS environments. Twenty-eight F2 progenies generated from an 8 x 8 half-diallel mating design were evaluated to determine combining ability effects and mode of gene action of grain yield (GYD) and yield attributing traits in navy bean under DS and non-stressed (NS) conditions. The experiments were conducted in two locations in a 6 x 6 square lattice design with two replications during the 2020 dry season. There were significant (p < 0.001; p < 0.05) positive correlations for number of pods per plant (NPPP), number of seeds per plant (NSPP) and 100-seed weight (SW) with GYD under both DS and NS. General and specific combining ability (GCA; SCA) effects were significant (p < 0.05) under both DS and NS for most traits indicating the importance of both additive and non-additive gene effects in the expression of the traits. Parents with best combining ability for most of the studied traits were G1, G7, G6 and G8 under NS, and G3, G4, G7 and G8 under DS. The most promising progenies with high values for GYD and its component traits under DS were G2 X G3, G2 X G8, G4 X G5, G4 X G8, and G6 X G8. Good general and specific combiners with high significant positive effects under DS should be used further in breeding for moisture stress tolerance.

scholarly journals A consensus map of chromosome 6R in rye (Secale cereale L.)

2009 ◽  
Vol 14 (2) ◽  
Author(s):  
Stefan Stojałowski ◽  
Beata Myśków ◽  
Paweł Milczarski ◽  
Piotr Masojć
Keyword(s):  
Molecular Markers ◽  
Software Package ◽  
Mapping Population ◽  
Average Distance ◽  
Rapid Development ◽  
Inbred Lines ◽  
Consensus Map ◽  
Marker Loci ◽  
Secale Cereale L ◽  
Mapping Populations

AbstractFour F2 mapping populations derived from crosses between rye inbred lines DS2×RXL10, 541×Ot1-3, S120×S76 and 544×Ot0-20 were used to develop a consensus map of chromosome 6R. Thirteen marker loci that were polymorphic in more than one mapping population constituted the basis for the alignment of the four maps using the JoinMap v. 3.0 software package. The consensus map consists of 104 molecular marker loci including RFLPs, RAPDs, AFLPs, SSRs, ISSRs, SCARs, STSs and isozymes. The average distance between the marker loci is 1.3 cM, and the total map length is 135.5 cM. This consensus map may be used as a source of molecular markers for the rapid development of new maps of chromosome 6R in any mapping population.

scholarly journals Evaluation of Maize (Zea mays L.) Hybrids for Economic Heterosis under Different Soil Moisture Regimes at North Eastern Plain Zone of India

2020 ◽  
pp. 55-67
Author(s):  
Ashok Singamsetti ◽  
J. P. Shahi ◽  
P. H. Zaidi ◽  
K. Seetharam ◽  
Kartik Madankar ◽  
...  
Keyword(s):  
Soil Moisture ◽  
Grain Yield ◽  
Agricultural Research ◽  
Moisture Stress ◽  
Maize Hybrids ◽  
Waterlogged Condition ◽  
Lattice Design ◽  
Standard Heterosis ◽  
Moisture Conditions ◽  
Positive Heterosis

The present experiment was conducted to understand the effect of soil moisture status on the economic or standard heterosis in fifty maize hybrids for grain yield and flowering traits.  The trials were planted at Agricultural Research Farm, Banaras Hindu University, Varanasi in alpha-lattice design with two replications. The analysis of variance revealed the significant differences for grain yield and flowering related traits such as days to 50% anthesis, days to 50% silking and anthesis-silking interval under all the moisture conditions including optimal, managed drought and managed waterlogging conditions. Significant amount of heterosis was observed over the selected check P3502 for all the traits under study; however, the magnitude and direction varied with traits and with soil moisture level. For days to 50% anthesis, hybrids ZH17192, VH112926, VH123021, ZH114250, ZH16929 and ZH16930 were showed significant negative heterosis under all the moisture conditions that explained earliness under both moisture-stress and normal conditions. Among the tested hybrids, VH123021 and ZH16929 were recorded significant negative standard heterosis for flowering traits; and significant positive heterosis for grain yield under all the three moisture conditions. Six hybrids under drought, seven hybrids under optimal and two hybrids under waterlogged condition showed positive standard heterosis for grain yield. Further evaluation of these hybrids at multi-locations and multi-year is advisable to confirm the promising findings observed in our study. This study could be valuable for development of climate-resilient maize hybrids.

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