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 Transcriptome Analysis of Distinct Cold Tolerance Strategies in the Rubber Tree (Hevea brasiliensis)

2018 ◽  
Author(s):  
Camila Campos Mantello ◽  
Lucas Boatwright ◽  
Carla Cristina da Silva ◽  
Erivaldo Jose Scaloppi ◽  
Paulo de Souza Gonçalves ◽  
...  
Keyword(s):  
Cold Tolerance ◽  
Hevea Brasiliensis ◽  
Amazon Basin ◽  
Rubber Tree ◽  
Tree Breeding ◽  
Snp Markers ◽  
Large Field ◽  
New Variety ◽  
Cold Response ◽  
Cold Temperatures

AbstractNatural rubber is an indispensable commodity used in approximately 40,000 products and is fundamental to the tire industry. Among the species that produce latex, the rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell-Arg.], a species native to the Amazon rainforest, is the major producer of latex used worldwide. The Amazon Basin presents optimal conditions for rubber tree growth, but the occurrence of South American leaf blight, which is caused by the fungus Microcyclus ulei (P. Henn) v. Arx, limits rubber tree production. Currently, rubber tree plantations are located in scape regions that exhibit suboptimal conditions such as high winds and cold temperatures. Rubber tree breeding programs aim to identify clones that are adapted to these stress conditions. However, rubber tree breeding is time-consuming, taking more than 20 years to develop a new variety. It is also expensive and requires large field areas. Thus, genetic studies could optimize field evaluations, thereby reducing the time and area required for these experiments. Transcriptome sequencing using next-generation sequencing (RNA-seq) is a powerful tool to identify a full set of transcripts and for evaluating gene expression in model and non-model species. In this study, we constructed a comprehensive transcriptome to evaluate the cold response strategies of the RRIM600 (cold-resistant) and GT1 (cold-tolerant) genotypes. Furthermore, we identified putative microsatellite (SSR) and single-nucleotide polymorphism (SNP) markers. Alternative splicing, which is an important mechanism for plant adaptation under abiotic stress, was further identified, providing an important database for further studies of cold tolerance.

scholarly journals QTL mapping of agronomic traits in wheat using the UK Avalon ×  Cadenza reference mapping population grown in Kazakhstan

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10733
Author(s):  
Akerke Amalova ◽  
Saule Abugalieva ◽  
Vladimir Chudinov ◽  
Grigoriy Sereda ◽  
Laura Tokhetova ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Agronomic Traits ◽  
Reference Population ◽  
Interval Mapping ◽  
Mapping Method ◽  
Kernel Weight ◽  
Snp Markers ◽  
Potential Yield ◽  
Dh Population ◽  
The Uk

Background The success of wheat production is largely dependent on local breeding projects that focus on the development of high-yielding cultivars with the use of novel molecular tools. One strategy for improving wheat productivity involves the deployment of diverse germplasms with a high potential yield. An important factor for achieving success involves the dissection of quantitative trait loci (QTLs) for complex agronomic traits, such as grain yield components, in targeted environments for wheat growth. Methods In this study, we tested the United Kingdom (UK) spring set of the doubled haploid (DH) reference population derived from the cross between two British cultivars, Avalon (winter wheat) and Cadenza (spring wheat), in the Northern, Central, and Southern regions (Karabalyk, Karaganda, Kyzylorda) of Kazakhstan over three years (2013–2015). The DH population has previously been genotyped by UK scientists using 3647 polymorphic DNA markers. The list of tested traits includes the heading time, seed maturation time, plant height, spike length, productive tillering, number of kernels per spike, number of kernels per meter, thousand kernel weight, and yield per square meter. Windows QTL Cartographer was applied for QTL mapping using the composite interval mapping method. Results In total, 83 out of 232 QTLs were identified as stable QTLs from at least two environments. A literature survey suggests that 40 QTLs had previously been reported elsewhere, indicating that this study identified 43 QTLs that are presumably novel marker-trait associations (MTA) for these environments. Hence, the phenotyping of the DH population in new environments led to the discovery of novel MTAs. The identified SNP markers associated with agronomic traits in the DH population could be successfully used in local Kazakh breeding projects for the improvement of wheat productivity.

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 De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways

PLoS ONE ◽  
2014 ◽  
Vol 9 (7) ◽  
pp. e102665 ◽  
Author(s):  
Camila Campos Mantello ◽  
Claudio Benicio Cardoso-Silva ◽  
Carla Cristina da Silva ◽  
Livia Moura de Souza ◽  
Erivaldo José Scaloppi Junior ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Hevea Brasiliensis ◽  
De Novo Assembly ◽  
De Novo ◽  
Rubber Tree ◽  
Snp Markers ◽  
Rubber Biosynthesis

scholarly journals Co- and post-translational processing of the hevein preproprotein of latex of the rubber tree (Hevea brasiliensis)

1991 ◽  
Vol 266 (24) ◽  
pp. 15944-15948
Author(s):  
H.I. Lee ◽  
W.F. Broekaert ◽  
N.V. Raikhel ◽  
H. Lee
Keyword(s):  
Hevea Brasiliensis ◽  
Rubber Tree

Bayesian Mapping of Multiple Quantitative Trait Loci From Incomplete Inbred Line Cross Data

Genetics ◽  
1998 ◽  
Vol 148 (3) ◽  
pp. 1373-1388
Author(s):  
Mikko J Sillanpää ◽  
Elja Arjas
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Composite Interval Mapping ◽  
Backcross Progeny ◽  
Random Variable ◽  
Interval Mapping ◽  
Mapping Method ◽  
Structure Mapping ◽  
Standard Interval ◽  
Trait Loci

Abstract A novel fine structure mapping method for quantitative traits is presented. It is based on Bayesian modeling and inference, treating the number of quantitative trait loci (QTLs) as an unobserved random variable and using ideas similar to composite interval mapping to account for the effects of QTLs in other chromosomes. The method is introduced for inbred lines and it can be applied also in situations involving frequent missing genotypes. We propose that two new probabilistic measures be used to summarize the results from the statistical analysis: (1) the (posterior) QTL-intensity, for estimating the number of QTLs in a chromosome and for localizing them into some particular chromosomal regions, and (2) the location wise (posterior) distributions of the phenotypic effects of the QTLs. Both these measures will be viewed as functions of the putative QTL locus, over the marker range in the linkage group. The method is tested and compared with standard interval and composite interval mapping techniques by using simulated backcross progeny data. It is implemented as a software package. Its initial version is freely available for research purposes under the name Multimapper at URL http://www.rni.helsinki.fi/~mjs.

scholarly journals A Rank-Based Nonparametric Method for Mapping Quantitative Trait Loci in Outbred Half-Sib Pedigrees: Application to Milk Production in a Granddaughter Design

Genetics ◽  
1998 ◽  
Vol 149 (3) ◽  
pp. 1547-1555 ◽  
Author(s):  
Wouter Coppieters ◽  
Alexandre Kvasz ◽  
Frédéric Farnir ◽  
Juan-Jose Arranz ◽  
Bernard Grisart ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Real Data ◽  
Interval Mapping ◽  
Mapping Method ◽  
Residual Variance ◽  
Data Set ◽  
Wilcoxon Rank Sum Test ◽  
Holstein Friesian ◽  
Trait Loci

Abstract We describe the development of a multipoint nonparametric quantitative trait loci mapping method based on the Wilcoxon rank-sum test applicable to outbred half-sib pedigrees. The method has been evaluated on a simulated dataset and its efficiency compared with interval mapping by using regression. It was shown that the rank-based approach is slightly inferior to regression when the residual variance is homoscedastic normal; however, in three out of four other scenarios envisaged, i.e., residual variance heteroscedastic normal, homoscedastic skewed, and homoscedastic positively kurtosed, the latter outperforms the former one. Both methods were applied to a real data set analyzing the effect of bovine chromosome 6 on milk yield and composition by using a 125-cM map comprising 15 microsatellites and a granddaughter design counting 1158 Holstein-Friesian sires.

scholarly journals Ethrel® stimulant increases the activity of soluble invertase isoforms in rubber tree (Hevea brasiliensis) bark tissues

2018 ◽  
Vol 12 (1) ◽  
pp. 99-107
Author(s):  
Débora Domiciano ◽  
◽  
Pollyanna Aparecida Carvalho ◽  
Luiz Edson Mota de Oliveira ◽  
Hilda Beatriz W. Cárdenaz ◽  
...  
Keyword(s):  
Hevea Brasiliensis ◽  
Rubber Tree

scholarly journals Expression and characterization of active site mutants of hevamine, a chitinase from the rubber tree Hevea brasiliensis

2002 ◽  
Vol 269 (3) ◽  
pp. 893-901 ◽  
Author(s):  
Evert Bokma ◽  
Henriëtte J. Rozeboom ◽  
Mark Sibbald ◽  
Bauke W. Dijkstra ◽  
Jaap J. Beintema
Keyword(s):  
Active Site ◽  
Hevea Brasiliensis ◽  
Rubber Tree ◽  
Active Site Mutants
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