chloroplast microsatellite
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2022 ◽  
Vol 31 (2) ◽  
pp. 115-122
Author(s):  
Rita Sarah Borna ◽  
S Mitra ◽  
AJA Gifary ◽  
RH Sarker

Biramsundari is a rice germplasm from Bangladesh showing one to four grain in a single seed. Comparative study of morphological traits revealed that BS is a taller rice variety compared to modern rice varieties with longer and wider flag leaves, longer panicle length and higher thousand seed weight (TSW) than transplanted aman rice variety BRRI dhan 49. Flower morphological analysis unveil that multiple grains of Biramsundari are originating from multiple number of carpels in each floret. About 40.1% flower contains three carpels. Fluorescent microscopic study also confirms the zygotic origin of multiple grain formation in Biramsundari. Molecular characterisation of Biramsundari was performed by using TeaCpSSR27 and TeaCpSSR28 chloroplast microsatellite markers. The results of this investigation reveal that atpF and rsp14-psaB intergenic spacer regions of Biramsundari have variation compared to sequences of with O. sativa ssp. indica, O. sativa ssp. japonica and O. rufipogon. Plant Tissue Cult. & Biotech. 31(2): 115-122, 2021 (December)


Forests ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1757
Author(s):  
Marina Sheller ◽  
Elena Ciocîrlan ◽  
Pavel Mikhaylov ◽  
Sergey Kulakov ◽  
Nadezhda Kulakova ◽  
...  

Scots pine is one of the dominant conifer species in forest ecosystems of the boreal zone in Eurasia. Knowledge of the genetic structure and the level of genetic variability of Scots pine populations is relevant for the development of measures aimed at conservation of species’ diversity. In this study, we used ten paternally inherited chloroplast microsatellite loci to investigate the genetic diversity of nineteen Scots pine populations from Middle Siberia and the Romanian Carpathians. The results of the study showed high genetic diversity (HCP = 0.91–1.00) in all of the investigated populations. The cpSSR analysis yielded a total of 158 haplotypes. The majority of the haplotypes (85%) were detected only once (unique haplotypes). Three common haplotypes were found between the Carpathian and the Siberian populations of Scots pine. Analysis of molecular variance (AMOVA) showed that only 3% of the variation occurred among populations from Middle Siberia and 6% of the variation existed among populations from the Carpathian Mountains. Overall, we found a weak geographic population structure in Scots pine from Middle Siberia and the Romanian Carpathians. The present study on genetic diversity in the Siberian and the Carpathian populations of Scots pine may contribute to the sustainable management and conservation of Scots pine genetic resources in Middle Siberia and the Romanian Carpathians.


2021 ◽  
Author(s):  
Relique Ignace AGBO ◽  
Antoine Missihoun ◽  
David Montcho ◽  
Rollande Dagba ◽  
Paulin Sédah ◽  
...  

Abstract The main objective of this study is to investigate the patterns of genetic diversity and phylogenetic relationships within populations of Detarium microcarpum (Fabaceae) relative to different spatial conditions. Seventy-eight (78) accessions of D. microcarpum belonging to six populations (Phytogeographic districts) were sampled. In order to have very good quality DNA for molecular analysis, an optimization of the DNA isolation protocol was made. The molecular analysis of the accessions was carried out using 7 chloroplast microsatellite markers. The polymorphism rate (P) is 85.71% and the Polymorphism Information Content (PIC) was in the range of 0.43 (Ntcp_9) to 0.73 (Ccmp_2) with an average of 0.59. Allelic richness (A) ranged from 1.41 to 2.85 with an average of 2.04. The observed heterozygosity (Ho) ranged from 0.23 to 0.60 with an average of 0.39. The expected heterozygosity (He) ranged from 0.43 to 0.60 with a mean of 0.50. Wright's fixation index (FIS) ranged from − 0.17 to 0.47. The effective allele (Ae) is between 1.77 and 2.53 with an average of 2.02. Wright differentiation index (FST) was 0.024. Phylogenetic analysis revealed that the NST value was significantly higher than the GST value (NST = 0.452; GST = 0.190; P < 0.05). A relatively low hd haplotype diversity is obtained (Hd = 0.320). AMOVA analysis showed that 17.35% of the variation existed within populations but 45.80% among populations within the species. Neighbor-Joining phylogenetic tree of D. microcarpum revealed three non-distinct clusters haplotypes showing the existence of gene flow between populations of the species. Our findings of genetic structure and gene flow of D. microcarpum populations based on different spatial conditions is caused by evolutionary forces such as scattering and pollination.


PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0255776
Author(s):  
Azucena Jiménez-Ramírez ◽  
Delphine Grivet ◽  
Juan José Robledo-Arnuncio

The estimation of recent gene flow rates among vast and often weakly genetically differentiated tree populations remains a great challenge. Yet, empirical information would help understanding the interaction between gene flow and local adaptation in present-day non-equilibrium forests. We investigate here recent gene flow rates between two large native Scots pine (Pinus sylvestris L.) populations in central Iberian Peninsula (Spain), which grow on contrasting edaphic conditions six kilometers apart from each other and show substantial quantitative trait divergence in common garden experiments. Using a sample of 1,200 adult and offspring chloroplast-microsatellite haplotypes and a Bayesian inference model, we estimated substantial male gametic gene flow rates (8 and 21%) between the two natural populations, and even greater estimated immigration rates (42 and 64%) from nearby plantations into the two natural populations. Our results suggest that local pollen shedding within large tree populations does not preclude long-distance pollen immigration from large external sources, supporting the role of gene flow as a homogenizing evolutionary force contributing to low molecular genetic differentiation among populations of widely distributed wind-pollinated species. Our results also indicate the high potential for reproductive connectivity in large fragmented populations of wind-pollinated trees, and draw attention to a potential scenario of adaptive genetic divergence in quantitative traits under high gene flow.


OENO One ◽  
2021 ◽  
Vol 55 (3) ◽  
Author(s):  
Manna Crespan ◽  
Daniele Migliaro ◽  
Simone Larger ◽  
Massimo Pindo ◽  
Massimo Palmisano ◽  
...  

Italy is one of the richest countries in terms of grapevine varietal assortment, and the Marche region in central Italy has an ancient winegrowing tradition. Increasing interest in autochthonous grapevine varieties prompted efforts to recover and identify local minor germplasm also in this region, and to search for pedigree relationships and determine the evolution of varietal assortment. In the present study this was done using nuclear and chloroplast microsatellite markers and SNP markers from the Vitis18kSNP chip. Eighteen new genotypes were found, of which seventeen belonged to well-known, less known and even unknown vines found to be specific to the Marche region. The rearranged pedigree highlighted the complex intertwining relationships between Marche varieties. Second-degree relationships were also derived. Some minor Marche varieties have increased the number of parent-offspring related members of Garganega, Sangiovese, Crepolino/Visparola and Sciaccarello, which are varieties already recognised as founders or recurrent parents of many Italian cultivars. Crepolino/Visparola was shown to be a key variety in the evolution of the Marche varietal assortment, having played the role of parent and grandparent, as explained by the presence of this genotype in the region in ancient times. Surprisingly, Semidano, a well-known Sardinian variety, played a clear role as parent or grandparent of three minor Marche varieties, testifying to its presence in central Italy in ancient times. Incrocio Bruni 54 was confirmed as an offspring of Sauvignon and Verdicchio, as declared by the breeder. The parentage of Lacrima was completed: this variety was found to be a spontaneous cross between Nera Rada and Aleatico.A dendrogram of genetic similarity clearly resembled the groups defined with the pedigree reconstruction and it gave an indication of the genetic similarity of the varieties excluded from the strictest parentage links.


2021 ◽  
pp. 125-133
Author(s):  
Г.Ю. Спотарь ◽  
С.А. Блинова ◽  
А.А. Шварцев ◽  
Я.И. Алексеев ◽  
С.М. Гориславец

С помощью молекулярно-генетических и ампелографических методов проведена идентификация сортов винограда, относящихся к наиболее распространенным в мире техническим сортам западно-европейского происхождения. Генотипирование образцов проводилось с использованием 9-ядерных и 3-хлоропластных микросателлитных маркеров. На основании полученных профилей, по данным базы VIVC было установлено, что образец № 2 является сортом Каберне-Совиньон, образец № 4 - сортом Рисланер. Профиль образца № 1 совпадает с профилем сорта Мерло, за исключением разницы в двух парах нуклеотидов (п.н.) в одном аллеле локуса VVMD27, что можно объяснить редким случаем мутации в микросателлитной последовательности и не является достаточным основанием утверждать, что образец № 1 и Мерло являются разными сортами. Генетические профили образцов № 3 и № 6 соответствовали сортам сортогруппы Темпранильо, № 5 - сортам сортогруппы Рислинг рейнский, №7 - сортам сортогруппы Пино черный. Сорта в сортогруппах, полученные в результате соматических мутаций (связанных в основном с окраской ягод), имели одинаковый профиль. Принадлежность образцов к указанным сортам в сортогруппах была подтверждена ампелографическим методом. Использование для идентификации сортов в сортогруппах 6-9-ти SSR-маркеров в сочетании с ампелографическими методами позволяет получить достоверные результаты без удорожания работ. Однако дифференциация клонов и сортов, полученных в результате соматических мутаций, только SSR-маркерами потребует значительного увеличения их количества на 1-2 порядка либо использования высоковариабельных SSR-маркеров, таких как VRG ( Vitis riparia Götzhof). Таким образом, целесообразен более целенаправленный поиск полиморфизмов непосредственно в генах, отвечающих за определенные хозяйственно ценные признаки. В случае возникновения отличия в окраске ягод для дифференциации возможно использовать полиморфизм локуса гена VvMybA1, при изменении во вкусе и аромате ягод - в локусе гена VviDXS, при изменении лигнификации семян - в локусе гена VviAGL11, при повышении устойчивости к заболеваниям - в локусах соответствующих генов резистентности. The identification of grapes related to the most widespread wine varieties of West-European origin was carried out using molecular-genetic and ampelographic methods. Genotyping of samples was provided using 9- nuclear and 3-chloroplast microsatellite markers. Basing on the profiles obtained according to the VIVC database, it was established that Sample No. 2 is a ‘Cabernet-Sauvignon’ variety, and Sample No. 4 is a ‘Rieslaner’ variety. The profile of Sample No. 1 coincides with the ‘Merlot’ profile, except for the difference in 2 base pairs (bp) in one allele of the VVMD27 locus, which can be explained by a rare case of mutation in microsatellite sequence, and is not a sufficient reason to insist that Sample No. 1 and the ‘Merlot’ are different varieties. The genetic profiles of Samples No. 3 and No. 6 corresponded to the varieties of ‘Tempranillo’ group, No. 5 - to the varieties of ‘Rhein Riesling’ group, and No. 7 - to the varieties of ‘Pinot Noir’ group. The varieties of the groups, obtained as a result of somatic mutations (mainly associated with color of berries), had the same profile. The ampelographic method confirmed the origin of samples in the mentioned groups of varieties. Using of 6-9-SSR-markers in combination with ampelographic methods to identify the varieties of groups allows obtaining reliable results without increasing the cost of work. However, differentiation of clones and varieties in groups with only SSR-markers will require a significant increase in their number by 1-2 orders, or using of highly variable SSR-markers, such as VRG ( Vitis riparia Götzhof). Thus, a more targeted search for polymorphisms directly in genes responsible for certain economically valuable traits is advisable. In case of occurrence a difference in the color of berries, it is possible to use for differentiation the polymorphism of VvMybA1 gene locus, when flavor and aroma of berries change - to use the VviDXS gene locus, when seed lignification changes - the VviAGL11 gene locus, when disease resistance increases - the loci of the corresponding resistance genes.


Diversity ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 249
Author(s):  
Helmuth Edisson Nieves-Orduña ◽  
Markus Müller ◽  
Konstantin V. Krutovsky ◽  
Oliver Gailing

The cacao tree (Theobroma cacao L.) is native to the Amazon basin and widely cultivated in the tropics to produce seeds, the valuable raw material for the chocolate industry. Conservation of cacao genetic resources and their availability for breeding and production programs are vital for securing cacao supply. However, relatively little is still known about the phylogeographic structure of natural cacao populations. We studied the geographic distribution of cpDNA variation in different populations representing natural cacao stands, cacao farms in Ecuador, and breeding populations. We used six earlier published cacao chloroplast microsatellite markers to genotype 233 cacao samples. In total, 23 chloroplast haplotypes were identified. The highest variation of haplotypes was observed in western Amazonia including geographically restricted haplotypes. Two observed haplotypes were widespread across the Amazon basin suggesting long distance seed dispersal from west to east in Amazonia. Most cacao genetic groups identified earlier using nuclear SSRs are associated with specific chloroplast haplotypes. A single haplotype was common in selections representing cacao plantations in west Ecuador and reference Trinitario accessions. Our results can be used to determine the chloroplast diversity of accessions and in combination with phenotypic assessments can help to select geographically distinctive varieties for cacao breeding programs.


Forests ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 592
Author(s):  
Bei Cui ◽  
Ping Deng ◽  
Sheng Zhang ◽  
Zhong Zhao

Ancient trees are famous for their life spans of hundreds or even thousands of years. These trees are rare, a testament to history and are important for scientific research. Platycladus orientalis, with the longest life span and a beautiful trunk, has become the most widely planted tree species and is believed to be sacred in China. Extensive declines in habitat area and quality pose the greatest threats to the loss of genetic diversity of ancient P. orientalis trees in the middle reaches of the Yellow River. Strengthening the protection of P. orientalis genetic resources is of great significance for the long-term development of reasonable conservation and breeding strategies. To better understand the genetic diversity and population structure of P. orientalis, we successfully analyzed four polymorphic chloroplast simple sequence repeat (cpSSR) loci and applied them to diversity and population structure analyses of 202 individuals from 13 populations in the middle reaches of the Yellow River. Based on the cpSSR data, 16 alleles were detected across 202 individuals, and a moderate level of genetic diversity was inferred from the genetic diversity parameters (H = 0.367 and AR = 1.964). The mean pairwise genetic differentiation coefficient (Fst) between populations was 0.153, indicating relatively high genetic population differentiations. Analysis of molecular variance (AMOVA) showed that only 8% of the variation occurred among populations. Structure analysis divided the 13 P. orientalis populations into two groups with no significant geographic population structure, which was consistent with the unweighted pair group method with arithmetic mean (UPGMA) and Mantel test results. These results may indicate that transplanting and cultivation by ancient human activities are the main factors responsible for the revealed pattern of genetic differentiation of ancient P. orientalis populations. Our research is of great significance for the future establishment of protection schemes and scientific breeding of P. orientalis.


2021 ◽  
Vol 81 (01) ◽  
pp. 93-100
Author(s):  
Md Aminul Islam ◽  
S. M. Shivaraj ◽  
Virender Kumar ◽  
Dinesh S. Phad ◽  
Humira Sonah ◽  
...  

In the present study, a total of 27 chloroplast specific SSRs (CpSSR) have been identified in the chloroplast genome of Capsicum annum L. The frequency of the SSRs was about one in 5.7 kb of the chloroplast genome. Out of 27 SSRs, 26 were mono-nucleotide repeats of A/T and one was a trinucleotide repeat (TTA). Further a set of seven markers were validated by genotyping 48 capsicum accessions comprising of cultivars from five different species and landraces of unknown identity. The seven SSR markers generated a total of 27 alleles among 48 samples used in this study. The size of the amplicons varied from 161 bp (CaCpM22 and 26) to 339 bp (CaCpM06). The polymorphic information content (PIC) value for the set of the primers used ranged from 0.11 to 0.48 with an average of 0.33. The number of alleles for markers ranged from three to six with an average of 3.28 alleles per marker. The phylogenetic analysis of the chilly accessions showed that the Bhut jolokia land race is clustered along with the C. frutescence indicating the it’s probable parentage. The chloroplast genome based SSR markers identified in the present study can be further used for the marker-assisted genomic studies


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