Comparative analysis of core collection sampling methods for mandarin germplasm based on molecular and phenotypic data. (1st October 2017)

• Record Type: Journal Article
• Authors: Garcia‐Lor, A.; Luro, F.; Ollitrault, P.; Navarro, L.
• Is Part Of: Annals of applied biology. Volume 171:Number 3(2017)
• Page Start: 327
• Page End: 339
• Publication Date: 2017-10-01
• Subjects: Citrus reticulata -- diversity -- genetic resources -- genotype -- molecular markers -- phenotype; Crop science -- Periodicals; Plants, Protection of -- Periodicals; Crops -- Ecology -- Periodicals; 630
• DOI: 10.1111/aab.12376
• Languages: English
• ISSNs: 0003-4746

Abstract

Abstract: Gene banks have been established to conserve the genetic diversity of crop species. Large germplasm collections lead to management problems (space, maintenance costs, etc.), especially in collections involving species with recalcitrant seeds that must be maintained as growing plants. Core collections (CCs) are thus developed to reduce the size of large germplasm collections while keeping the maximum variability. This also facilitates fine phenotypic evaluation. In this study, several software packages (DARwin, PowerMarker and MSTRAT) and methods (Max length subtree, M strategy, simulated annealing and MinSD) were compared to define a mandarin ( Citrus reticulata ) CC. One hundred and sixty‐seven accessions were sampled from two germplasm collections, which were genotyped with 50 SSR, 24 InDel and 68 single nucleotide polymorphism markers. All the CC obtained were tested for the maintenance of the genetic variability parameters (Ho and He) of the initial collection, the level of linkage disequilibrium (LD) and the phenotypic diversity retention. The Max length subtree function from DARWin seemed to be the most appropriate method for establishing a CC in C. reticulata . It maintained 96.82% of the allelic richness and 17.96% of the size of the initial collection with only 30 accessions. Besides it did not increase the LD ( r 2 value) of the initial collection and retained the vast majority of the phenotypic variability. However, a CC with 70 accessions would be more helpful for genetic association studies. Abstract : Comparative results of the core collection sampling methods in the two sizes selected (χ 2, P < 0.05). Germplasm collections are established to maintain the genetic diversity of the crops. When they are huge and are species with recalcitrant seeds as citrus, their maintenance, costs, space and so on become a problem. To reduce their size, but maintaining their diversity, core collections are being developed.