Genome-wide association mapping of latex yield and girth in Amazonian accessions of Hevea brasiliensis grown in a suboptimal climate zone

Chanroj, Vipavee; Rattanawong, Ratchanee; Phumichai, Thitaporn; Tangphatsornruang, Sithichoke; Ukoskit, Kittipat

doi:10.1016/j.ygeno.2017.07.005

Cited by 27 publications

(30 citation statements)

References 77 publications

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“…The average r 2 values were found to be very different when the two detected groups were compared. This measurement was higher in the breeding germplasm (0.49) than in the wild germplasm (0.02), corroborating the results of Chanroj et al (2017) , who suggested that these results were caused by high gene flow in the wild Amazonian population. The breeding accessions exhibited a notably higher level of LD, suggesting less genetic diversity in this subdivision, perhaps because of the constraint of genetic variability employed in breeding programs due to the recurrent process of selection.…”

Section: Discussionsupporting

confidence: 86%

“…The distances of LD decay between the two groups were most different in LGs 3, 5, 7, 10, and 11, suggesting that these chromosomes may carry more genes related to agronomic traits that have been selected via organized breeding of this crop. In previous studies involving Amazonian accessions of rubber tree, Chanroj et al (2017) revealed an LD decay of more than 0.5–6 cM and suggested that LD estimates were significantly influenced by physical distance, with LD decay greater than 2 kbp being observed in the widespread Amazonian population. These authors showed that LD decay over genetic distance was different for the 18 different chromosomes, possibly because of the different recombination rates of the 18 chromosomes.…”

Section: Discussionmentioning

confidence: 89%

“…For example, Le Guen et al (2009) demonstrated a separation between the Acre and Rondônia groups and the Mato Grosso group. One possible reason for this separation is that the wild accessions are from geographically distant populations that are not connected by hydrographic networks ( Le Guen et al, 2009 ; Chanroj et al, 2017 ), whereas most of the Wickham clones were collected from regions that are geographically closer to the Mato Grosso and the Tapajós river, enabling rubber seeds to flow from one region to another via the river. de Souza et al (2015) reported a difference in genotypes between the two groups, which are in different river basins, thus separating the genotypes in the cultivated and wild groups.…”

Section: Discussionmentioning

confidence: 99%

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Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis)

et al. 2018

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Among rubber tree species, which belong to the Hevea genus of the Euphorbiaceae family, Hevea brasiliensis (Willd. ex Adr.de Juss.) Muell. Arg. is the main commercial source of natural rubber production worldwide. Knowledge of the population structure and linkage disequilibrium (LD) of this species is essential for the efficient organization and exploitation of genetic resources. Here, we obtained single-nucleotide polymorphisms (SNPs) using a genotyping-by-sequencing (GBS) approach and then employed the SNPs for the following objectives: (i) to identify the positions of SNPs on a genetic map of a segregating mapping population, (ii) to evaluate the population structure of a germplasm collection, and (iii) to detect patterns of LD decay among chromosomes for future genetic association studies in rubber tree. A total of 626 genotypes, including both germplasm accessions (368) and individuals from a genetic mapping population (254), were genotyped. A total of 77,660 and 21,283 SNPs were detected by GBS in the germplasm and mapping populations, respectively. The mapping population, which was previously mapped, was constructed with 1,062 markers, among which only 576 SNPs came from GBS, reducing the average interval between two adjacent markers to 4.4 cM. SNPs from GBS genotyping were used for the analysis of genetic structure and LD estimation in the germplasm accessions. Two groups, which largely corresponded to the cultivated and wild populations, were detected using STRUCTURE and via principal coordinate analysis. LD analysis, also using the mapped SNPs, revealed that non-random associations varied along chromosomes, with regions of high LD interspersed with regions of low LD. Considering the length of the genetic map (4,693 cM) and the mean LD (0.49 for cultivated and 0.02 for wild populations), a large number of evenly spaced SNPs would be needed to perform genome-wide association studies in rubber tree, and the wilder the genotypes used, the more difficult the mapping saturation.

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Section: Discussionsupporting

confidence: 86%

Section: Discussionmentioning

confidence: 89%

Section: Discussionmentioning

confidence: 99%

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Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis)

et al. 2018

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“…In a suboptimal climate area with a lengthy dry season, Chanroj et al (2017) found a single SNP associated with girth accounting for 14% of the phenotypic variance in H. brasiliensis . Although this was not observed herein, the QTLs identified in our work can also be used as an initial source for marker-assisted selection because seven QTLs showed major effects (phenotypic variance greater than 10%) ( Table 5 ).…”

Section: Discussionmentioning

confidence: 93%

High-Resolution Genetic Map and QTL Analysis of Growth-Related Traits of Hevea brasiliensis Cultivated Under Suboptimal Temperature and Humidity Conditions

et al. 2018

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Rubber 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.

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“…) and was distributed via collections from Malaysia and Cote d'Ivoire. Between one and 18 individual trees had been collected from different municipalities (subsequently called “locations”), and clones from these trees were planted in 1994 with five replicates per clone in a spacing of 3 × 7 m. Trees were tapped regularly for latex (see Chanroj, Rattanawong, Phumichai, Tangphatsornruang, & Ukoskit, for details) and fertilized twice a year with 500 g N:P:K (30:5:18) fertilizer per tree, applied in the middle between tree rows.…”

Section: Methodsmentioning

confidence: 99%

Trait evolution in tropical rubber (Hevea brasiliensis) trees is related to dry season intensity

Rungwattana

Kasemsap

Phumichai³

et al. 2018

Functional Ecology

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Drought shapes the distribution and survival of trees even in tropical wet forests, and the wood and leaf trait spectra are used to understand drought adaptations. However, trait variation may result from ontogenetic adjustment or be related to tree size and not reflect evolutionary adaptations. Intraspecific variation in adaptations to drought can be an important factor in a species’ distribution and response to climate change, but excluding potentially confounding factors and proving adaptive evolution are challenging. Provenance trials can identify hereditary variability. We analysed wood and leaf traits in rubber (Hevea brasiliensis) tree clones from 15 locations in the Amazon basin that were planted in northern Thailand, controlled for tree size, tested for genetic relatedness and the phylogenetic signal in traits and compared trait variations with the climate at the location of origin. Correlations between traits and tree size were low. Intraspecific trait variation was similar to relationships in published among‐species comparisons, and correlations among wood traits and correlations among leaf traits were stronger than between wood and leaf traits. Genotype explained 30%–70% of the trait variation, and traits differed in how much of this variation was controlled by location or the relatedness among clones. There was no correlation with mean temperature or total annual rainfall. However, rainfall in the driest quarter (19–199 mm) was strongly related to leaf mass per area, carbon isotopic composition and area‐based nitrogen content (r2 = 0.54–0.70) and weaker to wood traits (vessel density and vessel lumen fraction). Trees from locations with a stronger dry season also had higher growth rates in Thailand. All traits correlating with climate showed a significant phylogenetic signal. We found no evidence of increased drought tolerance, but the trait spectrum and higher growth in trees from drier locations suggest that deciduous rubber trees have adapted via drought avoidance rather than tolerance. Our study also underlines the importance of looking at a suite of traits rather than individual ones to understand adaptive strategies. A http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.13203/suppinfo is available for this article.

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Genome-wide association mapping of latex yield and girth in Amazonian accessions of Hevea brasiliensis grown in a suboptimal climate zone

Cited by 27 publications

References 77 publications

Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis)

Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis)

High-Resolution Genetic Map and QTL Analysis of Growth-Related Traits of Hevea brasiliensis Cultivated Under Suboptimal Temperature and Humidity Conditions

Trait evolution in tropical rubber (Hevea brasiliensis) trees is related to dry season intensity

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