Ecotype-Level Genetic Biodiversity of Five Italian Traditional Crops

Italy displays a high level of agrobiodiversity due to its diversified pedoclimatic zones. The Administrative Region of Campania includes several and divergent biomes, occurring close to each other. In fact, the distance between a sea level environment and that of high mountains can be less than 20 km. These environmental conditions allow the cultivation of many different crops and vegetables, represented by diverse ecotypes and varieties that are well adapted to the distribution range where they have been selected and grown. Efforts to maintain and further increase biodiversity in farming systems require a better understanding of the existing diversity created by traditional farming practices. The aim of our study was to identify and molecularly characterize several ecotypes belonging to five horticultural species commonly cultivated in Campania. In particular, we analysed five ecotypes of maize, two of garlic, four of onion, one of escarole, and two of courgette by means of simple sequence repeat (SSR) markers in order to evaluate their level of genetic biodiversity. The results reveal, for the first time, the high genetic biodiversity of horticultural ecotypes of the Campania Region. This feature is very important to improve the quality and productivity of agroecosystems.

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Simple Sequence Repeat and S-Locus Genotyping to Assist the Genetic Characterization and Breeding of Polyploid Prunus Species, P. spinosa and P. domestica subsp. insititia

Biochemical Genetics ◽

10.1007/s10528-021-10090-7 ◽

2021 ◽

Author(s):

Júlia Halász ◽

Noémi Makovics-Zsohár ◽

Ferenc Szőke ◽

Sezai Ercisli ◽

Attila Hegedűs

Keyword(s):

Simple Sequence Repeat ◽

Principal Component ◽

Sequence Repeat ◽

Breeding Programs ◽

Allele Number ◽

Genetic Potential ◽

Ssr Loci ◽

High Level ◽

Diversity Studies ◽

Simple Sequence

AbstractPolyploid Prunus spinosa (2n = 4 ×) and P. domestica subsp. insititia (2n = 6 ×) represent enormous genetic potential in Central Europe, which can be exploited in breeding programs. In Hungary, 16 cultivar candidates and a recognized cultivar ‘Zempléni’ were selected from wild-growing populations including ten P. spinosa, four P. domestica subsp. insititia and three P. spinosa × P. domestica hybrids (2n = 5 ×) were also created. Genotyping in eleven simple sequence repeat (SSR) loci and the multiallelic S-locus was used to characterize genetic variability and achieve a reliable identification of tested accessions. Nine SSR loci proved to be polymorphic and eight of those were highly informative (PIC values ˃ 0.7). A total of 129 SSR alleles were identified, which means 14.3 average allele number per locus and all accessions but two clones could be discriminated based on unique SSR fingerprints. A total of 23 S-RNase alleles were identified and the complete and partial S-genotype was determined for 10 and 7 accessions, respectively. The DNA sequence was determined for a total of 17 fragments representing 11 S-RNase alleles. ‘Zempléni’ was confirmed to be self-compatible carrying at least one non-functional S-RNase allele (SJ). Our results indicate that the S-allele pools of wild-growing P. spinosa and P. domestica subsp. insititia are overlapping in Hungary. Phylogenetic and principal component analyses confirmed the high level of diversity and genetic differentiation present within the analysed accessions and indicated putative ancestor–descendant relationships. Our data confirm that S-locus genotyping is suitable for diversity studies in polyploid Prunus species but non-related accessions sharing common S-alleles may distort phylogenetic inferences.

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Simple Sequence Repeat Marker Analysis of Genetic Diversity among Progeny of a Biparental Mapping Population of Sweetpotato

HortScience ◽

10.21273/hortsci.50.8.1143 ◽

2015 ◽

Vol 50 (8) ◽

pp. 1143-1147 ◽

Cited By ~ 8

Author(s):

Benard Yada ◽

Gina Brown-Guedira ◽

Agnes Alajo ◽

Gorrettie N. Ssemakula ◽

Robert O.M. Mwanga ◽

...

Keyword(s):

Genetic Diversity ◽

Linkage Analysis ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Polymorphic Information Content ◽

Genetic Distances ◽

Sequence Repeat ◽

Population Improvement ◽

High Level ◽

Simple Sequence

Genetic diversity is critical in sweetpotato improvement as it is the source of genes for desired genetic gains. Knowledge of the level of genetic diversity in a segregating family contributes to our understanding of the genetic diversity present in crosses and helps breeders to make selections for population improvement and cultivar release. Simple sequence repeat (SSR) markers have become widely used markers for diversity and linkage analysis in plants. In this study, we screened 405 sweetpotato SSR markers for polymorphism on the parents and progeny of a biparental cross of New Kawogo × Beauregard cultivars. Thereafter, we used the informative markers to analyze the diversity in this population. A total of 250 markers were polymorphic on the parents and selected progeny; of these, 133 were informative and used for diversity analysis. The polymorphic information content (PIC) values of the 133 markers ranged from 0.1 to 0.9 with an average of 0.7, an indication of high level of informativeness. The pairwise genetic distances among the progeny and parents ranged from 0.2 to 0.9, and they were grouped into five main clusters. The 133 SSR primers were informative and are recommended for use in sweetpotato diversity and linkage analysis.

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Genetic variation in Hydrangea macrophylla (Thunb.) Ser. in Russia based on simple sequence repeat markers

Bangladesh Journal of Botany ◽

10.3329/bjb.v47i4.47389 ◽

2018 ◽

Vol 47 (4) ◽

pp. 937-943

Author(s):

Natalia Sukhikh ◽

Valentina Malyarovskaya ◽

Anastasiya Kamionskaya ◽

Lidia Samarina ◽

Svetlana Vinogradova

Keyword(s):

Simple Sequence Repeat ◽

Genetic Relationships ◽

Effective Number ◽

Sequence Repeat ◽

Base Pairs ◽

Breeding Programs ◽

Simple Sequence Repeat Markers ◽

Hydrangea Macrophylla ◽

High Level ◽

Simple Sequence

Genetic diversity and genetic relationships among 39 accessions of Hydrangea macrophylla (Thunb.) Ser. were analyzed using 38 previously developed simple sequence repeat markers (SSRs). A total of 38 polymorphic primers representing 166 bands with an average of 4.53 polymorphic bands per primer were selected. The number of alleles detected per locus ranged from two to eight with a total of 163 alleles amplified. The size of the amplified fragments ranged from 70 to180 base pairs. The effective multiallelic markers with high level of heterozygosity (more than 0.7) and effective number of alleles (more than 3.5) were identified. In this study nine SSR markers showed clear polymorphisms. The dendrogram grouped all hybrids in three major clusters, and two of these clusters included only mophead cultivars. The lacecap cultivars clustered more closely to each other. The results of this research could be used in breeding programs of H. macrophylla.

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The value of transhumance for biodiversity conservation: Vulture foraging in relation to livestock movements

AMBIO ◽

10.1007/s13280-021-01668-x ◽

2021 ◽

Author(s):

Natividad Aguilera-Alcalá ◽

Eneko Arrondo ◽

Roberto Pascual-Rico ◽

Zebensui Morales-Reyes ◽

José M. Gil-Sánchez ◽

...

Keyword(s):

Farming Systems ◽

Foraging Activity ◽

Farming Practices ◽

Wild Ungulates ◽

Traditional Farming ◽

Factors Affecting ◽

Seasonal Movements ◽

Gyps Fulvus ◽

Vulture Conservation ◽

Landscape Level

AbstractIn recent decades, intensive techniques of livestock raising have flourished, which has largely replaced traditional farming practices such as transhumance. These changes may have affected scavengers’ behaviour and ecology, as extensive livestock is a key source of carrion. This study evaluates the spatial responses of avian scavengers to the seasonal movements of transhumant herds in south-eastern Spain. We surveyed the abundance of avian scavengers and ungulates, and analysed the factors affecting the space use by 30 GPS-tracked griffon vultures (Gyps fulvus). Griffons’ foraging activity increased in the pasturelands occupied by transhumant herds, which implied greater vulture abundance at the landscape level during the livestock season. In contrast, facultative scavengers were more abundant without transhumant livestock herds, and the abundance of wild ungulates did not change in relation to livestock presence. We conclude that fostering transhumance and other traditional farming systems, to the detriment of farming intensification, could favour vulture conservation.

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Apple Proliferation Resistance in Apomictic Rootstocks and Its Relationship to Phytoplasma Concentration and Simple Sequence Repeat Genotypes

Phytopathology ◽

10.1094/phyto-98-2-0153 ◽

2008 ◽

Vol 98 (2) ◽

pp. 153-158 ◽

Cited By ~ 28

Author(s):

C. Bisognin ◽

B. Schneider ◽

H. Salm ◽

M. S. Grando ◽

W. Jarausch ◽

...

Keyword(s):

Simple Sequence Repeat ◽

Natural Infection ◽

Dna Typing ◽

Type I ◽

Type Ii ◽

Apple Proliferation ◽

Sequence Repeat ◽

Candidatus Phytoplasma Mali ◽

High Level ◽

Simple Sequence

In an effort to select and characterize apple rootstock resistant to apple proliferation (AP), progenies from seven apomictic rootstock selections and their parental apomictic species, Malus sieboldii and M. sargentii, were compared to standard stocks M 9 and M 11. Seedlings derived from open pollinated mother plants were grafted with cv. Golden Delicious and grown under natural infection conditions. The progenies differed greatly in resistance to the AP agent ‘Candidatus Phytoplasma mali’. Progenies of M. sieboldii and its descendent rootstock selections D2212, 4608, 4551, and D1131 showed a high level of resistance, whereas progenies of M. sargentii and its descendent selections D1111 and C1828 proved susceptible. M 9 and M 11 showed an intermediate level of resistance. Phytoplasma titer in roots of the M. sieboldii and M. sargentii progeny groups was similarly low, whereas the concentration in the standard stocks was 100 to 5,000 times higher. In trees on most of the resistant stocks, only a minority was colonized in the scion, while in trees on susceptible and standard stocks, infection rate was often higher. Also, the titer in the top of trees on resistant stocks was usually lower than in trees on susceptible and standard stocks. Four progenies derived from open pollinated M. sieboldii and M. sieboldii descendents were subjected to DNA typing using simple sequence repeat (SSR) markers. This study revealed that the selected groups consisted mainly of mother-like plants (apomicts) and type I hybrids (unreduced mother genotype plus one male allele at each locus). Type II hybrids (full recombinants) and autopollinated offspring were rare. In the 4608 progeny, trees grown on type I hybrid rootstocks were significantly less affected than trees on mother-like stocks. In other progenies with fewer or no type I hybrids, trees on type II hybrids and autopollinated offspring suffered considerably more from disease than trees on mother-like stocks.

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Genetic diversity of ten Moroccan populations of Tetraclinis articulata as revealed by Inter Simple Sequence Repeat (ISSR) markers

BOIS & FORETS DES TROPIQUES ◽

10.19182/bft2020.345.a31927 ◽

2020 ◽

Vol 345 ◽

pp. 15-25

Author(s):

Meryem MAKKAOUI ◽

Younes ABBAS ◽

Salwa EL ANTRY-TAZY ◽

Leila MEDRAOUI ◽

Mohammed ALAMI ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Mantel Test ◽

Conservation Strategies ◽

Sequence Repeat ◽

Tetraclinis Articulata ◽

High Level ◽

Simple Sequence

Tetraclinis articulata (Vahl) Masters is one of Morocco's most important forest species. It is also found occasionally in Malta and Spain, showing significant adaptability to different bio-climatic conditions. However, the species is being affected by anthropogenic fragmentation, logging and neglect from authorities, which could lead to the irretrievable loss of this resource. In this study, the genetic diversity and genetic structure of ten Moroccan populations of T. articulata were assessed. Fifteen Inter-Simple Sequence Repeat (ISSR) markers were used. These generated 271 polymorphic fragments with an average of 18.06 per primer and showed 79.59% of polymorphism. The 129 individuals revealed a high level of genetic diversity (Hs = 0.221; Ht = 0.254) and 85% of genetic variation within populations. However, the genetic differentiation level was low (Gst = 0.13), which is consistent with the lack of correlation between genetic and geographic distances revealed by the Mantel test, resulting in a high level of gene flow (Nm = 3.294). Based on PCoA and neighbour-joining methods, the ten populations clustered under the effect of continental and marine climates. Compared with other conifers, the current genetic diversity and the pattern of T. articulata population structure indicate an important gene pool requiring efficient conservation strategies.

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INTER-SIMPLE SEQUENCE REPEAT ANALYSIS AND ALLELIC DIVERSITY AMONG GENOTYPES OF CULTIVATED Digitaria species

Bangladesh Journal of Plant Breeding and Genetics ◽

10.3329/bjpbg.v30i2.32473 ◽

2018 ◽

Vol 30 (2) ◽

pp. 01-08

Author(s):

D. A. Animasaun ◽

K. F. Awujoola ◽

R. Krishnamurthy ◽

J. A. Morakinyo

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Similarity Index ◽

Allelic Diversity ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Sequence Repeat ◽

Simple Sequence Repeat Analysis ◽

First Time ◽

Simple Sequence

Acha (Digitaria exilis Kipps. and D. iburua Stapf.) are valuable indigenous food crops in West Africa, but despite several economic potentials of this crop, little or no attention is paid to its germplasm evaluation and improvement. In this study, we assessed genetic diversity and relationship among genotypes of cultivated acha in Nigeria using Inter-Simple Sequence Repeat (ISSR) markers for the first time. Genomic DNA were extracted from the genotypes and we performed fragment amplification by Polymerase Chain Reaction (PCR). A total of 95 loci consisting of 790 bands were amplified by 13 ISSR primers, out of which 53.37% were polymorphic. Loci amplification per primer ranged from 5-10, with an average of 7.30 loci per primer. Eight of the primers had above 50% polymorphism. Cluster analysis separated the genotypes into two major groups; a group consisting of two D. exilis genotypes and the other comprising a mixture of genotypes. The D. exilis in the latter group were distant members and was only similar at 0.72 similarity index. The polymorphism we obtained in the present study showed that the ISSR markers are effective for assessment of genetic diversity of the genotypes. Clustering of D. exilis and D. iburua together suggests a common progenitor but could have been separated by geographical isolation mechanism

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Molecular phylogeny of genus Musa determined by simple sequence repeat markers

Plant Genetic Resources ◽

10.1017/s1479262115000222 ◽

2015 ◽

Vol 14 (3) ◽

pp. 192-199 ◽

Cited By ~ 1

Author(s):

Huimin Feng ◽

You Chen ◽

Bo Li ◽

Yaoting Wu

Keyword(s):

Simple Sequence Repeat ◽

Polymorphic Information Content ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Molecular Data ◽

Sequence Repeat ◽

Wide Range ◽

Molecular Marker Analysis ◽

High Level ◽

Simple Sequence

Musa L. was previously separated into five sections (Eumusa, Rhodochlamys, Callimusa, Australimusa and Ingentimusa) based on basic chromosome numbers and morphological characters. However, several molecular analyses currently support restructuring of Musa species into two sections, Musa and Callimusa. The application of simple sequence repeat molecular marker analysis to Musa phylogeny provided valuable, supplemental information about the classification of, and relationships between, Musa species and subspecies. Totally, 28 accessions of Musa acuminata Colla subspecies and varieties and 25 accessions of other Musa species were evaluated; 12 primers produced 91 polymorphic bands, polymorphic information content ranged from 0.4473 to 0.8394 (average = 0.7226), indicating that the primers showed a high level of polymorphism. Our results generally agreed with previous phylogenetic analyses based on molecular data. One clade comprised species of sections Australimusa and Callimusa (X= 10/9); most species of sections Eumusa and Rhodochlamys (X= 11) formed the other clade. The relationships between most species were as expected; however, some species did not conform to findings of previous studies. A wide range of variability was observed in the M. acuminata complex. M. acuminata var. chinensis and M. acuminata subsp. 522 showed the most distant relationships to other subspecies: Musa laterita, Musa ornata and Musa velutina clustered with M. acuminata var. chinensis, suggesting that they may constitute a secondary gene pool for the improvement of cultivated bananas. Molecular data indicated that Musa tongbiguanensis Chen You & Yao-Ting Wu, which was observed and described by our research group in Yunnan, China, was a distinct, new species.

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Genetic differentiation of Allium sibiricum L. populations in Poland based on their morphological and molecular markers

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.3618 ◽

2019 ◽

Vol 88 (1) ◽

Author(s):

Jacek Urbaniak ◽

Paweł Kwiatkowski ◽

Bartosz Kozak

Keyword(s):

Simple Sequence Repeat ◽

Genetic Similarity ◽

Inter Simple Sequence Repeat ◽

Sequence Repeat ◽

The Carpathians ◽

Repeat Dna ◽

Local Range ◽

High Level ◽

Simple Sequence ◽

Simple Sequence Repeat Dna

Allium sibiricum is one of the rarest plant species in the Sudetes and Carpathians. Inter simple sequence repeat DNA (ISSR) and morphological analyses were conducted to study the biogeographical relationships between geographically disjunctive populations of A. sibiricum in the Carpathians and Sudetes. The results clearly differentiated the Carpathian and Sudetes populations, but also showed a relatively high level of genetic similarity in specimens within certain groups of the Sudetes and Carpathian populations. The plants collected in the Karkonosze probably belong to a mountain form of A. schoenoprasum morphotype C which inhabits natural sites there. In contrast, the study found morphologically and genetically different plants inhabiting Pilsko Mt in the Carpathians. The plants from the Carpathians were present in scattered sites probably due to the activity of Vlach shepherds and the formation of large pastures. The species enlarged its local range due to this type of anthropopressure and likely hybridized with the cultivated Allium plants introduced by the shepherds. This may indicate that the populations on Pilsko Mt are of a partly anthropogenic character.

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Comparative transcriptome analysis of the ovary and testis of the lacustrine goby (Gobiopterus lacustris)

10.1101/781104 ◽

2019 ◽

Author(s):

Zhongdian Dong ◽

Chengqin Huang ◽

Hairui Zhang ◽

Shunkai Huang ◽

Ning Zhang ◽

...

Keyword(s):

Simple Sequence Repeat ◽

Expression Patterns ◽

Gonadal Development ◽

Future Research ◽

Coastal Environments ◽

Comparative Transcriptome ◽

Brackish Waters ◽

Qpcr Analysis ◽

First Time ◽

Simple Sequence

ABSTRCTLacustrine goby (Gobiopterus lacustris) belongs to a genus of gobies that are small in size and endemic to freshwater, brackish waters or coastal environments around the Indian and Pacific oceans. To date, there are no genomic or transcriptomic studies on G. lacustris. Here, we constructed gonadal transcriptomes of G. lacustris for the first time and identified genes that may be involved in gonadal development and reproduction. In total, 60,657,644 and 52,016,136 clean reads were obtained from ovary and testis, respectively, using Illumina sequencing. Reads were assembled into 62,573 unigenes with N50 value of 3,082 bp and a mean length of 1,869 bp. A total of 47,891 (76.53%) unigenes were annotated in at least one of the seven databases that were used in this study. In addition, 38,550 SSRs (simple sequence repeat, microsatellite) were identified from 20,517 SSR containing sequences. Gene expression patterns in the testis and ovary were compared, and 10,954 DEGs (differentially expressed genes) were identified. Of these genes, 2,383 were up-regulated in the testis and 8,571 were up-regulated in the ovary. RT-qPCR analysis of 14 selected genes showed patterns consistent with the transcriptome results. Numerous DEGs involved in gonadal development and gametogenesis were identified, including foxl2, dmrt1, cyp19a1a, inha, inhb, sycp2, zglp1, tdrp, zps and esra. Using GO and KEGG enrichment analyses, pathways involving regulation of gonadal development and gametogenesis also identified. This work represents the first gonadal transcriptomic analysis of G. lacustris and provides a valuable dataset for future research on the genes involved in reproduction of G. lacustris.

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