Genetic structure analysis and selection of a core collection for carob tree germplasm conservation and management

Guardo, Mario Di; Scollo, Francesco; Ninot, A.; Rovira, M.; Hermoso, J.F.; Distefano, Gaetano; Malfa, Stefano La; Batlle, I.

doi:10.1007/s11295-019-1345-6

Cited by 32 publications

(36 citation statements)

References 43 publications

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“…Constructing core collections to represent the genetic spectrum of the whole population with maximum diversity and minimum redundancy appears to be an attractive choice for tree breeders and basic science researchers because a large-size collection can thereby be handled more efficiently and effectively for conservation and breeding purposes and other research objectives [43][44][45][46]. Many efforts have been invested in constructing core collections from fruit trees, such as grape (Vitis vinifera L. subsp.…”

Section: Discussionmentioning

confidence: 99%

Chinese Fir Breeding in the High-Throughput Sequencing Era: Insights from SNPs

Zheng

Wei

et al. 2019

Forests

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Knowledge on population diversity and structure is of fundamental importance for conifer breeding programs. In this study, we concentrated on the development and application of high-density single nucleotide polymorphism (SNP) markers through a high-throughput sequencing technique termed as specific-locus amplified fragment sequencing (SLAF-seq) for the economically important conifer tree species, Chinese fir (Cunninghamia lanceolata). Based on the SLAF-seq, we successfully established a high-density SNP panel consisting of 108,753 genomic SNPs from Chinese fir. This SNP panel facilitated us in gaining insight into the genetic base of the Chinese fir advance breeding population with 221 genotypes for its genetic variation, relationship and diversity, and population structure status. Overall, the present population appears to have considerable genetic variability. Most (94.15%) of the variability was attributed to the genetic differentiation of genotypes, very limited (5.85%) variation occurred on the population (sub-origin set) level. Correspondingly, low F ST (0.0285-0.0990) values were seen for the sub-origin sets. When viewing the genetic structure of the population regardless of its sub-origin set feature, the present SNP data opened a new population picture where the advanced Chinese fir breeding population could be divided into four genetic sets, as evidenced by phylogenetic tree and population structure analysis results, albeit some difference in membership of the corresponding set (cluster vs. group). It also suggested that all the genetic sets were admixed clades revealing a complex relationship of the genotypes of this population. With a step wise pruning procedure, we captured a core collection (core 0.650) harboring 143 genotypes that maintains all the allele, diversity, and specific genetic structure of the whole population. This generalist core is valuable for the Chinese fir advanced breeding program and further genetic/genomic studies. breeder to address the population genetic architecture (genetic structure, diversity and relationship, etc.) and facilitate the accurate mating designs with parental analysis to accelerate the breeding progress [8]. The accessible molecular marker includes: (1) hybridization-based type such as restriction fragment length polymorphism (RFLP) and its modified forms, (2) PCR and electrophoresis-based type including random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), sequence-related amplified polymorphism (SRAP), inter simple sequence repeat (ISSR), and simple sequence repeat (SSR) etc., and (3) sequencing-based type dominated by single nucleotide polymorphism (SNP) [9][10][11]. Of these, SNPs have proved to be the most abundant form of variation within a species at genome level that provides more detailed insights into the genetic base of a population [10]. They have become more and more popular because they can be high-throughput detected through next-generation sequencing (NGS) at a moderate cost. Notably, the NGS-based SNP genoty...

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Section: Discussionmentioning

confidence: 99%

Chinese Fir Breeding in the High-Throughput Sequencing Era: Insights from SNPs

Zheng

Wei

et al. 2019

Forests

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“…Ten clusters were tested ( k = 1–10) and the validation of the most likely number of clusters K was performed with the Structure Harvester following the ΔK method proposed by Evanno et al (2005) . Trees were assigned to a cluster when the membership coefficient was ≥ 0.8 ( Di Guardo et al, 2019 ).…”

Section: Methodsmentioning

confidence: 99%

“…The preference of farmers for a specific select phenotype, in the case of Cyprus for “Tillyria,” could pose an additional threat for the species’ genetic diversity ( Barracosa et al, 2007 ). However, the reviving interest in the carob warrants the investigation of its genetic diversity to establish conservation and breeding programs ( Di Guardo et al, 2019 ). Further to the classical studies on genetic diversity based on morphological traits ( Barracosa et al, 2007 ), the use of molecular markers caries the advantage that they are more polymorphic and unaffected by the environment.…”

Section: Introductionmentioning

confidence: 99%

“…Further to the classical studies on genetic diversity based on morphological traits ( Barracosa et al, 2007 ), the use of molecular markers caries the advantage that they are more polymorphic and unaffected by the environment. Microsatellites (SSRs) have been successfully used to assess carob genetic diversity ( La Malfa et al, 2014 ; Viruel et al, 2018 ; Di Guardo et al, 2019 ). Additionally, a prerequisite for revitalizing the carob industry is the assessment of the variation for morphological and compositional traits ( Barracosa et al, 2007 ; Custodio et al, 2011 ; Benchikh et al, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

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Pod Morphology, Primary and Secondary Metabolite Profiles in Non-grafted and Grafted Carob Germplasm Are Configured by Agro-Environmental Zone, Genotype, and Growing Season

et al. 2021

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Carob is a predominantly rainfed tree crop of high nutritive value and a long history of adaptation to the edaphoclimatic stress conditions of the Mediterranean. However, declining attention to the carob tree in recent decades has aggravated genetic erosion. The extant in situ germplasm varies both in terms of pod morphology and composition, reflecting the genetic and physiological divide chiefly among grafted and non-grafted material, and possibly the impact of variable agro-environments. Accordingly, the present study aimed to establish a systematic categorization of the genetic and phenotypic diversity encountered across carob germplasm identified in situ throughout Cyprus, a historical center of production and genetic diversity for the species. Linking pod morphology, primary and secondary metabolite profiles with genotyped source material originating in different agro-environments and crop seasons would provide a framework for interpreting (a) the interaction of these factors in configuring carob pod physicochemical constitution, and (b) the relative stability of phenotypic traits against environmental and seasonal variation. Microsatellite analysis discriminated 36 genotypes out of the 124 trees located in nine traditional agro-environmental zones and revealed low genetic diversity within the grafted germplasm. Two landraces were identified: “Tillyria,” which is widespread and predominant, and “Kountourka,” which is mainly localized to the northeastern peninsula of Karpasia. Morphological traits, such as seeds-to-pod weight ratio, pod width and thickness were principally under genetic control. Contrarily, compositional traits, particularly total phenolic content—including condensed tannins, in vitro antioxidant capacity and to a lesser extent gallic acid, organic acids and minerals were under agro-environmental control. Agro-environmental zone also modulated principally fructose and glucose; sucrose was modulated equally by genotype and agro-environment, while total sugars were under genetic control. Statistically significant differences between seasons were detected for all traits except for the seeds-to-pod weight ratio, pod length and width. Hierarchical cluster analysis corroborates that Cyprus may be divided into two major agro-environmental zones modulating the compositional properties of the carob pulp. The present study provides a comprehensive insight into the extant carob genetic resources of Cyprus and advances our understanding of how genetic, agro-environmental and seasonal factors interact in shaping carob pod morphology and composition.

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“…Unusual heavy pest infestations on large branches and trunks, associated with serious decline and wilting, have been recently observed on carob trees in Sicily (Southern Italy) [ 29 – 31 ]. Carob is a thermophilous arboreal species characteristic of the olea-lentisc and carob groups (belonging to the Oleo sylvestris-Ceratonion siliquae alliance) [ 32 ] and it is a widespread and long-living tree in Mediterranean woodland vegetation [ 33 , 34 ]. This tree species, largely diffused in dry areas of Sicily, provides to farmers several products and by-products including the flour extracted from the seeds (Locust Bean Gum, LBG) used in food industry as thickening agent (E410) [ 35 – 37 ].…”

Section: Introductionmentioning

confidence: 99%

Seasonal changes in population structure of the ambrosia beetle Xylosandrus compactus and its associated fungi in a southern Mediterranean environment

et al. 2020

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Exotic ambrosia beetles are increasing in Europe due to global trade and global warming. Among these xylomycetophagous insects, Xylosandrus compactus (Eichhoff) (Coleoptera: Curculionidae) is a serious threat for several Mediterranean host plants. Carob trees growing in Sicily (Italy) have been extensively attacked by beetles leading to rapid tree decline. Although X. compactus has been found in Europe for several years, most aspects of its ecology are still unknown. We thus studied the population structure and dynamics of X. compactus, together with its twig size preference during a sampling of infested carob trees in south east Sicily. In addition, fungi associated with insects or galleries were isolated and characterized. The results showed that, in this newly-colonized environment and host plant, adult X. compactus overwinters inside twigs and starts to fly and reproduce in mid spring, completing five generations before overwintering in late fall. The mean diameter of carob twigs infested by the beetle varied significantly over the seasons, with the insect tending to infest larger twigs as season progresses. The mean number of adults/gallery was 19.21, ranging from 6 to 28. The minimum temperature significantly affected the overwintering adult mortality. Ambrosiella xylebori and Fusarium solani were the main symbionts associated with the pest in this study. Acremonium sp. was instead recorded for the first time in Europe inside X. compactus galleries. Several other fungi species were also found for the first time in association with X. compactus. Our findings provide useful insights into the sustainable management of this noxious pest.

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Genetic structure analysis and selection of a core collection for carob tree germplasm conservation and management

Cited by 32 publications

References 43 publications

Chinese Fir Breeding in the High-Throughput Sequencing Era: Insights from SNPs

Chinese Fir Breeding in the High-Throughput Sequencing Era: Insights from SNPs

Pod Morphology, Primary and Secondary Metabolite Profiles in Non-grafted and Grafted Carob Germplasm Are Configured by Agro-Environmental Zone, Genotype, and Growing Season

Seasonal changes in population structure of the ambrosia beetle Xylosandrus compactus and its associated fungi in a southern Mediterranean environment

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