Abstract
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.
Highlights
The single-nucleotide polymorphisms (SNPs) identified from genotyping by sequencing (GBS) were uniformly distributed across the genetic map, resulting in improvements in group assessment and shortening of gaps compared with the base map (Figure 1)
GT1 is known by its climate resistance response (Moreno et al, 2005; Priyadarshan et al, 2009; Cheng et al, 2015) and suitable to be used in a study which aimed quantitative trait loci (QTL) mapping for drought tolerance
Using open-pollinated progenies from a mother tree of interest facilitated the development of progeny and accelerated linkage map construction and QTL detection, as in sweet cherries (Guajardo et al, 2015)
Summary
Adr. de Juss.) Muell-Arg., known as the rubber tree, is one of the most symbolic species from the Amazon basin owing to its worldwide use in natural latex production, the global demand for which suggests expansion of the industry (Warren-Thomas et al, 2015). It is a perennial and allogamous tree from the Euphorbiaceae family. Several methods were proposed, including maximum likelihood estimators for all types of markers segregation (Maliepaard et al, 1997) and the possibility to build integrated genetic maps using information from all available markers with multipoint estimation (Wu et al, 2002a,b). QTL mapping for complex traits related to plant growth (stem diameter, tree height, and number of whorls) was performed over a 59-month evaluation period, allowing for more accurate QTL localization
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