scholarly journals Physical Mapping of QTL in Four Spring Wheat Populations under Conventional and Organic Management Systems. I. Earliness

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 853
Author(s):  
Kassa Semagn ◽  
Muhammad Iqbal ◽  
Hua Chen ◽  
Enid Perez-Lara ◽  
Darcy H. Bemister ◽  
...  
Keyword(s):  
Spring Wheat ◽  
Physical Map ◽  
Interval Mapping ◽  
Snp Markers ◽  
Genetic Maps ◽  
Management Systems ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Data ◽  
Organic Management ◽  
Hard Red Spring Wheat

In previous studies, we reported quantitative trait loci (QTL) associated with the heading, flowering, and maturity time in four hard red spring wheat recombinant inbred line (RIL) populations but the results are scattered in population-specific genetic maps, which is challenging to exploit efficiently in breeding. Here, we mapped and characterized QTL associated with these three earliness traits using the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.0 physical map. Our data consisted of (i) 6526 single nucleotide polymorphisms (SNPs) and two traits evaluated at five conventionally managed environments in the ‘Cutler’ × ‘AC Barrie’ population; (ii) 3158 SNPs and two traits evaluated across three organic and seven conventional managements in the ‘Attila’ × ‘CDC Go’ population; (iii) 5731 SilicoDArT and SNP markers and the three traits evaluated at four conventional and organic management systems in the ‘Peace’ × ‘Carberry’ population; and (iv) 1058 SNPs and two traits evaluated across two conventionally and organically managed environments in the ‘Peace’ × ‘CDC Stanley’ population. Using composite interval mapping, the phenotypic data across all environments, and the IWGSC RefSeq v2.0 physical maps, we identified a total of 44 QTL associated with days to heading (11), flowering (10), and maturity (23). Fifteen of the 44 QTL were common to both conventional and organic management systems, and the remaining QTL were specific to either the conventional (21) or organic (8) management systems. Some QTL harbor known genes, including the Vrn-A1, Vrn-B1, Rht-A1, and Rht-B1 that regulate photoperiodism, flowering time, and plant height in wheat, which lays a solid basis for cloning and further characterization.

scholarly journals High-resolution genetic map and QTL analysis of growth-related traits of Hevea brasiliensis cultivated under suboptimal temperature and humidity conditions

2018 ◽  
Author(s):  
André Ricardo Oliveira Conson ◽  
Cristiane Hayumi Taniguti ◽  
Rodrigo Rampazo Amadeu ◽  
Isabela Aparecida Araújo Andreotti ◽  
Livia Moura de Souza ◽  
...  
Keyword(s):  
Hevea Brasiliensis ◽  
Rubber Tree ◽  
Tree Height ◽  
Interval Mapping ◽  
Mapping Method ◽  
Snp Markers ◽  
Genetic Maps ◽  
Stem Diameter ◽  
Breeding Cycle ◽  
Phenotypic Traits

AbstractRubber tree (Hevea brasiliensis) cultivation is the main source of natural rubber worldwide and has been extended to areas with suboptimal climates and lengthy drought periods; this transition affects growth and latex production. High-density genetic maps with reliable markers support precise mapping of quantitative trait loci (QTL), which can help reveal the complex genome of the species, provide tools to enhance molecular breeding, and shorten the breeding cycle. In this study, QTL mapping of the stem diameter, tree height, and number of whorls was performed for a full-sibling population derived from a GT1 and RRIM701 cross. A total of 225 simple sequence repeats (SSRs) and 186 single-nucleotide polymorphism (SNP) markers were used to construct a base map with 18 linkage groups and to anchor 671 SNPs from genotyping by sequencing (GBS) to produce a very dense linkage map with small intervals between loci. The final map was composed of 1,079 markers, spanned 3,779.7 cM with an average marker density of 3.5 cM, and showed collinearity between markers from previous studies. Significant variation in phenotypic characteristics was found over a 59-month evaluation period with a total of 38 QTLs being identified through a composite interval mapping method. Linkage group 4 showed the greatest number of QTLs (7), with phenotypic explained values varying from 7.67% to 14.07%. Additionally, we estimated segregation patterns, dominance, and additive effects for each QTL. A total of 53 significant effects for stem diameter were observed, and these effects were mostly related to additivity in the GT1 clone. Associating accurate genome assemblies and genetic maps represents a promising strategy for identifying the genetic basis of phenotypic traits in rubber trees. Then, further research can benefit from the QTLs identified herein, providing a better understanding of the key determinant genes associated with growth of Hevea brasiliensis under limiting water conditions.

scholarly journals Mapping Quantitative Trait Loci onto Chromosome-Scale Pseudomolecules in Flax

2020 ◽  
Vol 3 (2) ◽  
pp. 28 ◽  
Author(s):  
Frank M. You ◽  
Sylvie Cloutier
Keyword(s):  
Quantitative Trait Loci ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Quantitative Traits ◽  
Snp Markers ◽  
Genetic Maps ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Trait Loci ◽  
Genomic Regions

Quantitative trait loci (QTL) are genomic regions associated with phenotype variation of quantitative traits. To date, a total of 313 QTL for 31 quantitative traits have been reported in 14 studies on flax. Of these, 200 QTL from 12 studies were identified based on genetic maps, the scaffold sequences, or the pre-released chromosome-scale pseudomolecules. Molecular markers for QTL identification differed across studies but the most used ones were simple sequence repeats (SSRs) or single nucleotide polymorphisms (SNPs). To uniquely map the SSR and SNP markers from different references onto the recently released chromosome-scale pseudomolecules, methods with several scripts and database files were developed to locate PCR- and SNP-based markers onto the same reference, co-locate QTL, and scan genome-wide candidate genes. Using these methods, 195 out of 200 QTL were successfully sorted onto the 15 flax chromosomes and grouped into 133 co-located QTL clusters; the candidate genes that co-located with these QTL clusters were also predicted. The methods and tools presented in this article facilitate marker re-mapping to a new reference, genome-wide QTL analysis, candidate gene scanning, and breeding applications in flax and other crops.

scholarly journals Discovery of Single Nucleotide Polymorphisms for Resistance to Abnormal Vertical Growth in Macadamia

2021 ◽  
Vol 12 ◽  
Author(s):  
Mohamed Cassim Mohamed Zakeel ◽  
Mobashwer Alam ◽  
Andrew D. W. Geering ◽  
Bruce Topp ◽  
Olufemi A. Akinsanmi
Keyword(s):  
Disease Management ◽  
Genetic Markers ◽  
Mixed Model ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Data ◽  
Single Nucleotide ◽  
Mixed Model Analysis ◽  
Vertical Growth ◽  
Lack Of Information

Abnormal vertical growth (AVG) syndrome is a serious threat to the Australian macadamia industry as it decreases the yield of nuts by as much as 70% per annum. A lack of information on the cause of AVG has hindered the development of an effective disease management strategy. Discovery of genetic markers associated with disease resistance can be used as tool for rapid selection of elite cultivars, hence helps in efficient disease management. Differences in field susceptibility of macadamia cultivars provide an opportunity for discovery of genetic markers that are associated with host resistance. REML mixed model analysis was performed to estimate the AVG rating of 51 cultivars from multiple origins using phenotypic data from 359 trees planted in four sites. Most of the Hawaiian cultivars were found as susceptible, while selections from the Australian macadamia industry breeding program were predominantly resistant. All the cultivars were genotyped for 13,221 DArTseq-based single nucleotide polymorphism (SNP) markers. A bulked sample analysis was performed using 20 genotypes each at the extremes of AVG phenotypic ratings. Ten SNP markers were predicted to be associated with AVG resistance and two arbitrarily selected SNP markers were validated using PCR and Sanger sequencing. Our findings suggest that AVG resistance in the commercial cultivars may be derived from the genomic introgression of Macadamia tetraphylla through interspecific hybridization. The results may support marker-assisted selection for macadamia germplasm with AVG resistance.

Genome-based prediction of agronomic traits in spring wheat under conventional and organic management systems

2021 ◽  
Author(s):  
Kassa Semagn ◽  
Muhammad Iqbal ◽  
José Crossa ◽  
Diego Jarquin ◽  
Reka Howard ◽  
...  
Keyword(s):  
Spring Wheat ◽  
Agronomic Traits ◽  
Management Systems ◽  
Organic Management

scholarly journals Mapping Quantitative Trait Loci Associated With Graft (In)Compatibility in Apricot (Prunus armeniaca L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Ana Pina ◽  
Patricia Irisarri ◽  
Pilar Errea ◽  
Tetyana Zhebentyayeva
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Woody Plants ◽  
Molecular Mechanisms ◽  
Prunus Persica ◽  
Snp Markers ◽  
Genetic Maps ◽  
Phenotypic Data ◽  
Trait Loci ◽  
Genomic Regions

Graft incompatibility (GI) between the most popular Prunus rootstocks and apricot cultivars is one of the major problems for rootstock usage and improvement. Failure in producing long-leaving healthy grafts greatly affects the range of available Prunus rootstocks for apricot cultivation. Despite recent advances related to the molecular mechanisms of a graft-union formation between rootstock and scion, information on genetic control of this trait in woody plants is essentially missing because of a lack of hybrid crosses, segregating for the trait. In this study, we have employed the next-generation sequencing technology to generate the single-nucleotide polymorphism (SNP) markers and construct parental linkage maps for an apricot F1 population “Moniqui (Mo)” × “Paviot (Pa)” segregating for ability to form successful grafts with universal Prunus rootstock “Marianna 2624”. To localize genomic regions associated with this trait, we genotyped 138 individuals from the “Mo × Pa” cross and constructed medium-saturated genetic maps. The female “Mo” and male “Pa” maps were composed of 557 and 501 SNPs and organized in eight linkage groups that covered 780.2 and 690.4 cM of genetic distance, respectively. Parental maps were aligned to the Prunus persica v2.0 genome and revealed a high colinearity with the Prunus reference map. Two-year phenotypic data for characters associated with unsuccessful grafting such as necrotic line (NL), bark and wood discontinuities (BD and WD), and an overall estimate of graft (in)compatibility (GI) were collected for mapping quantitative trait loci (QTLs) on both parental maps. On the map of the graft-compatible parent “Pa”, two genomic regions on LG5 (44.9–60.8 cM) and LG8 (33.2–39.2 cM) were associated with graft (in)compatibility characters at different significance level, depending on phenotypic dataset. Of these, the LG8 QTL interval was most consistent between the years and supported by two significant and two putative QTLs. To our best knowledge, this is the first report on QTLs for graft (in)compatibility in woody plants. Results of this work will provide a valuable genomic resource for apricot breeding programs and facilitate future efforts focused on candidate genes discovery for graft (in)compatibility in apricot and other Prunus species.

scholarly journals Consensus Genetic Linkage Map Construction Based on One Common Parental Line for QTL Mapping in Wheat

Agronomy ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 227
Author(s):  
Xin Hu ◽  
Yingquan Zhang ◽  
Jingjuan Zhang ◽  
Shahidul Islam ◽  
Maoyun She ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Positional Cloning ◽  
Coat Color ◽  
Physical Map ◽  
Wheat Breeding ◽  
Snp Markers ◽  
Genetic Maps ◽  
Parental Line ◽  
Seed Color ◽  
Consensus Map

The consensus map is used for the verification of marker order, quantitative trait locus (QTL) mapping and molecular marker-assisted selection (MAS) in wheat breeding. In this study, a wheat consensus genetic map named as Sp7A_G7A, was constructed using 5643 SNP markers in two double haploid (DH) populations of Spitfire × Bethlehem-7AS (Sp7A) and Gregory × Bethlehem-7AS (G7A), covering 4376.70 cM of 21 chromosomes (chr) with an average interval of 0.78 cM. The collinearity of the linkage maps with the consensus map of Con_map_Wang2014 and the physical map of wheat reference genome (IWGSC RefSeq v1.0) were analyzed based on the Spearman rank correlation coefficients. As results, the three constructed genetic maps of Sp7A, G7A and Sp7A_G7A showed high collinearity with the Con_map_Wang2014 and the physical map, and importantly, the collinearity level between our constructed maps and the wheat physical map is higher than that between the Con_map_Wang2014 and the physical map. The seed coat color QTL detected in both populations under multiple environments were on the region (745.73–760.14 Mbp) of the seed color gene R-B1/Tamyb10-B1 (TraesCS3B02G515900, 3B: 757,918,264–757,920,082 bp). The validated consensus map will be beneficial for QTL mapping, positional cloning, meta-QTL analysis and wheat breading.

Registration of ‘Duclair’ Hard Red Spring Wheat

2011 ◽  
Vol 5 (3) ◽  
pp. 349-352 ◽  
Author(s):  
S. P. Lanning ◽  
G. R. Carlson ◽  
P. F. Lamb ◽  
D. Nash ◽  
D. M. Wichman ◽  
...  
Keyword(s):  
Spring Wheat ◽  
Hard Red Spring Wheat

Hybrid Vigor in Hard Red Spring Wheat Crosses 1

Crop Science ◽  
1970 ◽  
Vol 10 (3) ◽  
pp. 220-223 ◽  
Author(s):  
Darrell. G. Wells ◽  
Charles L. Lay
Keyword(s):  
Spring Wheat ◽  
Hybrid Vigor ◽  
Hard Red Spring Wheat
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