Genetic diversity in cultivated yam bean (Pachyrhizus spp.) evaluated through multivariate analysis of morphological and agronomic traits

Genet Resour Crop Evol (2018) 65:811–843 https://doi.org/10.1007/s10722-017-0582-5 RESEARCH ARTICLE Genetic diversity in cultivated yam bean (Pachyrhizus spp.) evaluated through multivariate analysis of morphological and agronomic traits A. Séraphin Zanklan . Heiko C. Becker . Marten Sørensen . Elke Pawelzik . Wolfgang J. Grüneberg Received: 22 June 2016 / Accepted: 7 October 2017 / Published online: 28 December 2017 © The Author(s) 2017. This article is an open access publication Abstract Yam bean [Pachyrhizus DC.] is a legume genus of the subtribe Glycininae with three root crop species [P. erosus (L.) Urban, P. tuberosus (Lam.) Spreng., and P. ahipa (Wedd.) Parodi]. Two of the four cultivar groups found in P. tuberosus were studied: the roots of ‘Ashipa’ cultivars with low root dry matter (DM) content similar to P. erosus and P. ahipa are traditionally consumed raw as fruits, Electronic supplementary material The online version of this article (doi:https://doi.org/10.1007/ s10722-017-0582-5) contains supplementary material, which is available to authorized users. A. S. Zanklan (&) Département de Biologie Végétale, Faculté des Sciences et Techniques, Université d´Abomey-Calavi, 01 BP 526, Cotonou, Benin e-mail: H. C. Becker Department of Crop Sciences, Göttingen University, Von-Siebold-Str. 8, 37075 Göttingen, Germany M. Sørensen Section for Organismal Biology, Faculty of Life Sciences, Copenhagen University, Thorvaldsensvej 40, 3, 1870 Frederiksberg C, Denmark E. Pawelzik Department of Crop Sciences, Göttingen University, Carl-Sprengel-Weg 1, 37075 Göttingen, Germany W. J. Grüneberg Department of Genetic Resources and Crop Improvement, International Potato Center, P.B. 1558, Lima 12, Peru whereas ‘Chuin’ cultivars with high root DM content are cooked and consumed like manioc roots. Interspecific hybrids between yam bean species are generally completely fertile. This study examines the genetic diversity of the three crop species, their potentials for breeding and the identification of useful traits to differentiate among yam bean genotypes and accessions. In total, 34 entries (genotypes and accessions) were grown during 2000–2001 at two locations in Benin, West Africa, and 75 morphological and agronomical traits, encompassing 50 quantitative and 25 qualitative characters were measured. Diversity between entries was analyzed using principal component analysis, cluster analysis, multivariate analysis of variance and discriminant function analysis. Furthermore, phenotypic variation within and among species was investigated. Intraand interspecific phenotypic diversity was quantified using the Shannon–Weaver diversity index. A character discard was tested by variance component estimations and multiple regression analysis. Quantitative trait variation ranged from 0.81 (for total harvest index) to 49.35% (for no. of storage roots per plant). Interspecific phenotypic variation was higher than intraspecific for quantitative traits in contrast to qualitative characters. Phenotypic variation was higher in overall for quantitative than qualitative traits. In general, intraspecific phenotypic variation ranged from 0.00 to 82.61%, and from 0.00 to 80.03% for quantitative and qualitative traits, respectively. Interspecific phenotypic variation ranged from 123 812 0.00 to 95.02%, and 0.00–81.58% for the two trait types, respectively. The Shannon–Weaver diversity index (H′) was in general high and over 0.80 for most of the trait. Diversity within P. tuberosus was higher than within P. erosus and P. ahipa. Across the 50 quantitative and 25 qualitative traits, the Shannon– Weaver diversity index of intra- and interspecific variation was around 0.83 and 0.51, respectively and was lower for qualitative than for quantitative traits. Monomorphism was observed in eight qualitative traits and one quantitative character. The first, second and third principal components explained, respectively, 39.1, 21.3 and 8.3% of the total variation in all traits. Pachyrhizus erosus, P. ahipa, and P. tuberosus (‘Chuin’ and ‘Ashipa’) were clearly separated from each other by these analyses. Multivariate analysis of variance indicates significant differences between Pachyrhizus species for all individual or grouped traits. Discriminant function analysis revealed that the first two discriminant functions were almost significant. Biases due to unbalanced sample size used per species were small. Within each species a similar amount of diversity was observed and was determinable to 70% by only ten traits. We conclude that the cultivated yam bean species represent distinct genepools and each exhibits similarly large amounts of genetic diversity. Keywords Agronomic traits · Genetic diversity · Yam bean · West Africa Abbreviations BIOM Total biomass DFA Discriminant function analysis MVA Multivariate analysis MANOVA Multivariate analysis of variance PV Phenotypic variation SEEY Seed yield SRDY Storage root dry matter yield Introduction Many thousands of plant species can be used by humanity, and around a hundred have been developed into crops. However, as only a few crops are widely grown today research interest into the so-called underutilized crops is rapidly growing—among them the yam beans (Pachyrhizus spp.). The nearest relative of economic importance is the soybean 123 Genet Resour Crop Evol (2018) 65:811–843 (Glycine max (L.) Merr.) and the levels of oil and protein of yam bean seeds resemble those typical of soybean (Grüneberg et al. 1999). Formerly, the genus Pachyrhizus was placed in the subtribe Diocleinae in close relationship to the subtribe Glycininae and Phaseolinae (Lackey 1977; Ingham 1990), but based on chloroplast DNA restriction site mapping, it was transferred to the subtribe Glycininae (Bruneau et al. 1994; Polhill 1994). Within the Glycininae, the yam bean shows a close relationship to tropical kudzu (Pueraria phaseoloides (Roxb.) Benth.) and other genera with a chromosome base number of x = 11 (Lee and Hymowitz 2001; Kumar and Hymowitz 1987). The yam bean species are diploid (2n = 22), self-pollinating (up to 8% cross pollination) and native to South and Central America (Sørensen 1990). The genus is defined as a homogeneous entity due to the stigma structure having a median to subterminal globular process on the adaxial side, the short hairs on the adaxial side of the ovary extending almost to the stigma, and the formation of storage roots (Sørensen 1988). Unlike its close relative, the soybean, the yam bean is exclusively used for its storage roots (Ramos-de-la-Peña et al. 2013). The use of yam bean seeds as source of biodegradable insecticide is also of potential economic interest due to their high rotenone contents (Lautié et al. 2012). The crop is the most important storage-root-forming legume, as its productivity is high and it has also high protein content in the storage roots (NRC 1979). In the cultivated species, due to the roots’ high moisture content, and (...truncated)