Genetic diversity analyses of rubber tree genotypes based on UPOV descriptors

https://doi.org/10.1016/j.indcrop.2021.113416Get rights and content

Highlights

  • For the first time for rubber tree breeding, this work investigates the genetic diversity techniques for morphological traits.

  • This work introduces methodologies to quantify genetic dissimilarity matrices and importance of morphological traits.

  • The descriptors leaf cluster, length, intensity of green color and leaf undulation of margin are sufficient to characterize the variability in the data analyzed.

  • The clones have a large genetic variability among themselves, highlighting the importance of preserving the clones in the field.

Abstract

The present study evaluated 57 genotypes of rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell. Arg.] utilizing 33 morphological descriptors at juvenile stage to determine importance for phenotypic characterization. This study compares different dissimilarity matrices and proposes a new way of calculating the distance matrix of multicategory descriptor traits; and a new way of analyzing importance of multicategorical traits. All the studied genotypes were obtained from the Rubber Tree Research Center and Agroforestry Systems' germplasm collection, which belongs to the Agronomic Institute (IAC), São Paulo State, Brazil.The results of the Mantel test showed a greater correlation between the complement of the simple and weighted similarity coefficients (0.94), followed by the similarity coefficient and Euclidean distance (0.75) and, finally, the Euclidean distance and the weighted similarity coefficient (0.62). The weighted similarity coefficient was the dissimilarity matrix that best represented the genetic diversity of the clones used, allowing the separation of the genotypes into 18 groups through Tocher grouping, demonstrating the genetic diversity present in the evaluated material. The morphoagronomic characterization of the accessions detected polymorphisms for all the evaluated traits, showing that the genotypes exhibited genetic variability for the 33 evaluated descriptors. The results obtained by the Shannon-Weaver and fingerprint analyses indicate that the use of the descriptors leaf cluster, leaf length, intensity of green color of leaf, leaf undulation of margin, and trunk diameter is sufficient to characterize the variability in the data analyzed. The comparison between the similarity indices used showed that the weighted similarity coefficient is at least similar to the similarity coefficient and seems to better represent genetic diversity. The IAC clones demonstrate large genetic variability among themselves, highlighting the success of the genetic improvement program as well as the importance of preserving clones in the field.

Introduction

The rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss. Müell. Arg)] is native to the Amazon valley and is responsible for 90% of the world’s supply of natural latex, which is irreplaceable in many products, such as medical devices, surgical gloves, and aircraft and car tires (Priyadarshan, 2017a). In addition, since the introduction of Henry Wickham material in 1876, Southeast Asia has become the major producer of natural rubber (Sobha et al., 2019). Most cultivars originating from the so-called Wickham germplasm were collected in the Amazonian region and introduced to Asia at the end of the nineteenth century. Therefore, the genetic basis of the cultivated material is quite narrow, even if most of the cultivars currently exhibit sufficient allelic diversity to allow for substantial genetic improvement (Priyadarshan, 2017b).

The increase in deforestation rates in the Amazon (Rochedo et al., 2018; Qin et al., 2019) is a concern for the entire rubber sector throughout the world. Since the country contains two-thirds of the remaining tropical forests of the Amazon, the current deforestation has resulted in large global extensions of forest loss and the associated loss of biodiversity (Imazon, 2020). This issue is a major concern for all those interested in the genetic improvement of rubber trees. The loss of genetic variability in in situ conservation increased the importance of studying and maintaining ex situ conservation that could enable future genetic improvement of genotypes adapted to different conditions (Le Guen et al., 2009) and avoid loss of diversity through genetic erosion due to extensive cultivation of a few so-called high-yielding varieties (Priyadarshan, 2016).

Currently, rubber tree breeding programs in Brazil are mainly conducted in the State of São Paulo. The Agronomic Institute (IAC) has been responsible for carrying out genetic improvement efforts for rubber trees in Brazil (Gonçalves et al., 2002, 2007, Gonçalves de et al., 2011; Goncalves et al., 2008). The breeding program currently has more than 500 new rubber tree clones under evaluation, with a total of 35 experiments distributed in five regional sites in the state of São Paulo, many of which have high production and other important traits such as girth, bark thickness; number of latex vessel rings; and others. Some of these genotypes are Wickham germplasm descendants from Southern Asia introduced in 1952 in IAC. Others are primary materials originating from prospections in the Amazon region (Le Guen et al., 2009). Understanding the genetic diversity that exists in this population is crucial to the success of conservation and breeding programs (Le Guen et al., 2009). In particular, the number of rubber clones grown in the world for rubber production is less than one hundred (Priyadarshan, 2016).

Genetic diversity studies of rubber tree genotypes have been conducted in Brazil (Le Guen et al., 2009; Gouvêa et al., 2010a, 2010b; Perseguini et al., 2012; Souza et al., 2015) mainly using molecular markers. Despite the importance, morphological and molecular markers have been reported as complementary to understand genetic diversity (Darkwa et al., 2020). Researchers have shown that studies of morphological traits play an important role in determining the genetic diversity in rubber tree (Rao et al., 2013; Oktavia et al., 2017; Adifaiz et al., 2018). Therefore, this type of study has never been reported in Brazil. Although the expression of morphological traits depends largely on the developmental phase, environmental factors, and applied cultivation techniques (Bhandari et al., 2017), morphological traits are a useful tool for the preliminary evaluation of genetic diversity. Additionally, the use of them is essential at the final breeding stage, which includes cultivar protection under breeder ownership rights (Gomes et al., 2020).

A standard approach applied to study genetic diversity is the comparison of individual genotypes within and between populations using a genetic dissimilarity matrix of all potential pairwise combinations of individuals for the characterization of population structure based on the relative affinity of everyone to all other individuals evaluated. Several measures, including Euclidean, Mahalanobis and Cole-Rogers, are frequently employed in the analysis of dissimilarity of individuals using quantitative phenotypic traits (Cruz et al., 2020). Gower (1971) proposed a technique that allows the simultaneous analysis of quantitative and qualitative data. However, in cases where the traits are multicategory, there are some similarity coefficients that are defined differently and so may produce different results. Hence, the choice of an appropriate similarity index is crucial for determining actual genetic dissimilarity among individuals and will consequently affect the cluster techniques that will be used to study genetic variability (Cruz et al., 2020). Thus, some authors have used the similarity index Gower metric coefficient (Oliveira et al., 2015; Agre et al., 2019; Adifaiz et al., 2020; Darkwa et al., 2020), Shannon-Weaver diversity index (Rao et al., 2013; Baldanzi et al., 2014; Mursyidin et al., 2019; Adifaiz et al., 2020; Darkwa et al., 2020; Stojanović and Magazin, 2020), Euclidian distance (Gomes et al., 2020; Ramos Ospino et al., 2020) and similarity coefficient (Quesada-Méndez et al., 2011). There is a lack of information about which technique is the best to study descriptors and/or multicategory traits. Therefore, it was decided in this research to propose a new methodology and compare different similarity indices applied to morphological descriptors.

The objectives of this study were to (1) compare different dissimilarity matrices, (2) propose a new way to calculate the distance for multicategory traits as well as a new way of analyzing the importance of these descriptors (3) characterize and quantify the variability of descriptors proposed by the International Union for the Protection of New Varieties of Plants (UPOV) in the Hevea germplasm collection in the Center of Rubber Tree and Agroforestry Systems, (4) assess the genetic diversity and differentiation of UPOV descriptors in the Hevea collection

Section snippets

Material and methods

A total of 57 genotypes were used in this study, and the genealogy of these genotypes is described in Table 1. The selected genotypes consisted of Asiatic (RRIM, PM, PB), African (IRCA) and Brazilian germplasms (IAC, IAN). Most of the Asiatic genotypes were derived from the Wickham germplasm collection originally introduced to Asia in 1876. The Brazilian genotype IAN 873 was crossed between PB 86 and the Ford clone FA1717 performed by the North Agronomic Institute (IAN) and Ford. The IAC clones

Genetic diversity

Initially, the correlation of the three distance matrices (Euclidean distance matrix, distance matrix of the complement of the similarity coefficient and the complement of the similarity coefficient weighted) was evaluated by the Mantel test to determine whether there was a difference between them. The way in which each matrix computes the diversity between genotypes is different, as shown in Fig. 1. The result of the Mantel test showed a greater correlation between the complement of the simple

Genetic diversity

The genetic improvement of important traits in plant breeding depends on the genetic diversity available within crop species. Thus, the genetic diversity of the 57 rubber tree genotypes was studied using UPOV morphological descriptors, enabling the formation of distinct groups for the IAC series and Asiatic genotypes. The three methodologies used in the study of genetic diversity between genotypes have important differences that must be considered when the researcher is interested in the

Conclusions

The comparison between the similarity indices used showed that the weighted genetic similarity coefficient is at least similar to the similarity coefficient and seems to better represent genetic diversity.

The proposed technique for the study of multicategorical traits is important since it allows the identification of genotype variability in relation to UPOV descriptors, just as the proposed fingerprint technique is efficient at determining the importance of descriptors in assessing genetic

Credit author statements

Isabela de Castro Sant’Anna: Writing - Reviewing and Editing, Software, Methodology, Formal analysis, Software, Methodology, Formal anlysis. Ligia R. L. Gouvêa: Writing and Editing, Methodology. José E. Scaloppi Junior: involved in certain parts of experiments. Rogério S. de Freitas: involved in certain parts of experiments. Paulo de Souza Gonçalves: provided critical feedback and delineated the research.

All authors provided helped shape the analysis and research and gave approval to the final

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgments

The authors gratefully acknowledge the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) (2018/18300-4) for financial supports and researcher fellowship to ICS (2018/26408-0) and, the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for the financial support (400130/2016-5).

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