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

Abstract

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.

Unravelling Rubber Tree Growth by Integrating GWAS and Biological Network-Based Approaches

“…The large number of SNP markers discovered in this work allowed us to assess the LD throughout the genome of the entire population in a very representative way. As in other studies using arboreal and allogamous species (Peláez et al, 2020), our results showed high LD, which is consistent with previous H. brasiliensis results (Chanroj et al, 2017;De Souza et al, 2018). Interestingly, such elevated decay is not constant, and regions with a high density of TEs present a lower level of LD compared to the overall genomic LD.…”

“…Furthermore, the genome of rubber trees encompasses a large number of repetitive regions, reaching approximately 71% of rubber tree genomic content (Tang et al, 2016). The first Hevea reference genome at the chromosome level was only recently published in 2020 (Liu et al, 2020a), and most genomic approaches in the species have been based on highly fragmented sequences and biocomputational estimations (Pootakham et al, 2015;Chanroj et al, 2017;Conson et al, 2018;de Souza et al, 2018;Souza et al, 2019). Only with the advent of molecular biology techniques for reducing genomic complexities during sequencing procedures, such as GBS (Elshire et al, 2011;Poland and Rife, 2012), has it been feasible to generate thousands of SNP markers with high frequency in complex plant genomes (Pootakham et al, 2015).…”

“…Using this approach, we were able to access all important molecular levels for the definition of SD. Despite the great economic importance of the species, as it is the only one capable of producing natural rubber in sufficient quantity and quality to supply the world market for this product (Ding et al, 2020), its genetic studies are still quite limited due to the complexity of its genome (Tang et al, 2016), its great genetic variability (De Souza et al, 2018) and the large areas needed for its plantation. Despite all these limitations, this work overcomes these difficulties, producing data, results and new methodological perspectives for future genomic studies in this species and identifying markers and genes useful for genetic improvement.…”

Population genetic structure and marker–trait associations in East and West African Striga hermonthica with varying phenotypic response to Fusarium oxysporum f. sp. strigae isolates Foxy‐2 and FK3

“…The SSR loci (Y53 and E1009) associated with the S. hermonthica group demonstrating susceptibility to both Foxy‐2 and FK3 represent promising candidates for developing stable molecular genetic markers for identifying S. hermonthica with susceptibility to both Foxy‐2 and FK3. The relatively high LD uncovered between SSR loci pairs in this S. hermonthica class with susceptibility to both Foxy‐2 and FK3 (compared with the other class demonstrating intermediate susceptibility/non‐susceptibility to either Foxy‐2 or FK3) paves the way for further LD mapping to gain deeper insights into the genes underlying this trait (Weir, 2008; de Souza et al ., 2018).…”

Identification of Candidate Gene-Based Markers for Girth Growth in Rubber Trees

“…The low linkage disequilibrium (LD) was also reported in the Amazonian population. Successful application of genome scanning to outcrossing species such as rubber tree will require a very high number of markers, making the candidate gene method more attractive [ 1 , 2 ]. The candidate gene approach has proven successful in many instances, such as in Arabidopsis [ 3 ] wheat [ 4 , 5 ], pea [ 6 ], potato [ 7 ], and perennial ryegrass [ 8 ].…”