Development of EST-SSR Markers and Association Mapping with Floral Traits in Syringa oblata

Abstract Background Lilac (Syringa oblata) is an important woody plant with high ornamental value. However, very limited genetic marker resources are currently available, and little is known about the genetic architecture of important ornamental traits for S. oblata, which is hindering its genetic studies. Therefore, it is of great significance to develop effective molecular markers and understand the genetic architecture of complex floral traits for the genetic research of S. oblata. Results In this study, a total of 10,988 SSRs were obtained from 9864 unigene sequences with an average of one SSR per 8.13 kb, of which di-nucleotide repeats were the dominant type (32.86%, 3611). A set of 2042 primer pairs were validated, out of which 932 (45.7%) exhibited successful amplifications, and 248 (12.1%) were polymorphic in eight S. oblata individuals. In addition, 30 polymorphic EST-SSR markers were further used to assess the genetic diversity and the population structure of 192 cultivated S. oblata individuals. Two hundred thirty-four alleles were detected, and the PIC values ranged from 0.23 to 0.88 with an average of 0.51, indicating a high level of genetic diversity within this cultivated population. The analysis of population structure showed two major subgroups in the association population. Finally, 20 significant associations were identified involving 17 markers with nine floral traits using the mixed linear model. Moreover, marker SO104, SO695 and SO790 had significant relationship with more than one trait. Conclusion The results showed newly developed markers were valuable resource and provided powerful tools for genetic breeding of lilac. Beyond that, our study could serve an efficient foundation for further facilitate genetic improvement of floral traits for lilac.

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Development of EST-SSR Markers and Association Mapping with Floral Traits in Syringa oblata

10.21203/rs.3.rs-20358/v3 ◽

2020 ◽

Author(s):

Yunyao Yang ◽

Ruiqing He ◽

Jian Zheng ◽

Zenghui Hu ◽

Jing Wu ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Genetic Architecture ◽

Genetic Research ◽

Mixed Linear Model ◽

Floral Traits ◽

Dominant Type ◽

High Level ◽

Nucleotide Repeats

Abstract Background: Lilac (Syringa oblata) is an important woody plant with high ornamental value. However, very limited genetic marker resources are currently available, and little is known about the genetic architecture of important ornamental traits for S. oblata, which is hindering its genetic studies. Therefore, it is of great significance to develop effective molecular markers and understand the genetic architecture of complex floral traits for the genetic research of S. oblata.Results: In this study, a total of 10,988 SSRs were obtained from 9,864 unigene sequences with an average of one SSR per 8.13 kb, of which di-nucleotide repeats were the dominant type (32.86%, 3,611). A set of 2,042 primer pairs were validated, out of which 932 (45.7%) exhibited successful amplifications, and 248 (12.1%) were polymorphic in eight S. oblata individuals. In addition, 30 polymorphic EST-SSR markers were further used to assess the genetic diversity and the population structure of 192 cultivated S. oblata individuals. 234 alleles were detected, and the PIC values ranged from 0.23 to 0.88 with an average of 0.51, indicating a high level of genetic diversity within this cultivated population. The analysis of population structure showed two major subgroups in the association population. Finally, 20 significant associations were identified involving 17 markers with nine floral traits using the mixed linear model. Moreover, marker SO104, SO695 and SO790 had significant relationship with more than one trait.Conclusion: The results showed newly developed markers were valuable resource and provided powerful tools for genetic breeding of lilac. Beyond that, our study could serve an efficient foundation for further facilitate genetic improvement of ﬂoral traits for lilac.

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Development of EST-SSR Markers and Association Mapping with Floral Traits in Syringa Oblata

10.21203/rs.3.rs-20358/v1 ◽

2020 ◽

Author(s):

Yunyao Yang ◽

Ruiqing He ◽

Jian Zheng ◽

Zenghui Hu ◽

Jing Wu ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Genetic Architecture ◽

Genetic Research ◽

Mixed Linear Model ◽

Floral Traits ◽

Dominant Type ◽

High Level ◽

Nucleotide Repeats

Abstract Background: Lilac (Syringa oblata) is an important woody plant with high ornamental value. However, very limited genetic marker resources are currently available, and little is known about the genetic architecture of important ornamental traits for S. oblata, which is hindering its genetic studies. Therefore, it is of great significance to develop effective molecular markers and understand the genetic architecture of complex floral traits for the genetic research of S. oblata.Results: In this study, a total of 10,988 SSRs were obtained from 9,864 unigene sequences with an average of one SSR per 8.13 kb, of which di-nucleotide repeats were the dominant type (32.86%, 3,611). A set of 2,042 primer pairs were validated, out of which 932 (45.7%) exhibited successful amplifications, and 248 (12.1%) were polymorphic in eight S. oblata individuals. In addition, 30 polymorphic EST-SSR markers were further used to assess the genetic diversity and the population structure of 192 cultivated S. oblata individuals. 234 alleles were detected, and the PIC values ranged from 0.23 to 0.88 with an average of 0.51, indicating a high level of genetic diversity within this cultivated population. The analysis of population structure showed two major subgroups in the association population. Finally, 20 significant associations were identified involving 17 markers with nine floral traits using the mixed linear model. Moreover, marker SO104, SO695 and SO790 had significant relationship with more than one trait.Conclusion: The results showed newly developed markers were valuable resource and provided powerful tools for genetic breeding of lilac. Beyond that, our study could serve an efficient foundation for further facilitate genetic improvement of ﬂoral traits for lilac.

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Genetic Diversity and Population Structure Revealed by SSR Markers on Endemic Species Osmanthus serrulatus Rehder from Southwestern Sichuan Basin, China

Forests ◽

10.3390/f12101365 ◽

2021 ◽

Vol 12 (10) ◽

pp. 1365

Author(s):

Lin Chen ◽

Tingting Pan ◽

Huirong Qian ◽

Min Zhang ◽

Guodong Yang ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Sichuan Basin ◽

Polymorphic Information Content ◽

Population Decline ◽

Natural Populations ◽

Genetic Population ◽

Endangered Status ◽

High Level

Osmanthus serrulatus Rehder (Oleaceae) is an endemic spring-flowering species in China. It is narrowly distributed in the southwestern Sichuan Basin, and is facing the unprecedented threat of extinction due to problems associated with natural regeneration, habitat fragmentation and persistent and serious human interference. Here, the genetic diversity and population structure of 262 individuals from ten natural populations were analyzed using 18 microsatellites (SSR) markers. In total, 465 alleles were detected across 262 individuals, with a high polymorphic information content (PIC = 0.893). A high level of genetic diversity was inferred from the genetic diversity parameters (He = 0.694, I = 1.492 and PPL = 98.33%). AMOVA showed that a 21.55% genetic variation existed among populations and the mean pairwise Fst (0.215) indicated moderate genetic population differentiation. The ten populations were basically divided into three groups, including two obviously independent groups. Our results indicate that multiple factors were responsible for the complicated genetic relationship and endangered status of O. serrulatus. The concentrated distribution seems to be the key factor causing endangerment, and poor regeneration, human-induced habitat loss and fragmentation seem to be the primary factors in the population decline and further genetic diversity loss. These findings will assist in future conservation management and the scientific breeding of O. serrulatus.

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Assessment of the genetic diversity and population structure of apricot (Prunus armeniaca L.) germplasm of the Northwestern Himalaya using SSR markers

Plant Genetic Resources ◽

10.1017/s1479262121000459 ◽

2021 ◽

pp. 1-10

Author(s):

Aijaz A. Wani ◽

Khalid Hussain ◽

Showkat A. Zargar ◽

Faizan Ahmad ◽

Reetika Mahajan ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Geographical Location ◽

Prunus Armeniaca ◽

Resolving Power ◽

Diversity Assessment ◽

Prunus Armeniaca L ◽

Genetic Pool ◽

High Level

Abstract Apricot is considered an ecologically and economically important tree species of the stone-fruit crops that is widely grown in temperate regions of the world. Very few studies on apricot genetic diversity assessment have been carried out from the regions of Kashmir and Ladakh. In this backdrop, the present study was carried out to analyse the genetic diversity and population structure of 120 apricot genotypes collected from both the regions using 21 SSR markers. A total of 52 alleles were amplified with average values of marker index (MI) = 0.7084, resolving power (RP) = 2.8690, polymorphism information content (PIC) = 0.3132, Na = 2.317, Ne = 1.720, I = 0.572, Ho = 0.284, He = 0.360 and an average polymorphism of 91.2% per assay indicating high level of genetic diversity. The neighbour-joining (NJ) dendrogram generated three main clusters among selected apricot genotypes independent of their geographical locations. Interestingly, the result of the dendrogram coincides with the results of structure analysis which showed that the 120 apricot genotypes could be assigned to three (K = 3) sub-populations and the grouping of genotypes did not follow their geographical location suggesting that they share the same genetic pool. Moreover, analysis of molecular variance showed that 73% of the variation was attributed to differences within the individuals, 25% among individuals while only 2% of the variation was observed among the populations. The present study represents the most comprehensive analysis of the genetic diversity and population structure of apricot genotypes in Kashmir and Ladakh regions of India.

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High-Level Genetic Diversity and Complex Population Structure of Siberian Apricot (Prunus sibirica L.) in China as Revealed by Nuclear SSR Markers

PLoS ONE ◽

10.1371/journal.pone.0087381 ◽

2014 ◽

Vol 9 (2) ◽

pp. e87381 ◽

Cited By ~ 25

Author(s):

Zhe Wang ◽

Ming Kang ◽

Huabo Liu ◽

Jiao Gao ◽

Zhengdong Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Complex Population ◽

Siberian Apricot ◽

Nuclear Ssr ◽

High Level

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Genetic Diversity and Population Structure of Japanese Plum-Type (Hybrids of P. salicina) Accessions Assessed by SSR Markers

Agronomy ◽

10.3390/agronomy11091748 ◽

2021 ◽

Vol 11 (9) ◽

pp. 1748

Author(s):

Brenda I. Guerrero ◽

M. Engracia Guerra ◽

Sara Herrera ◽

Patricia Irisarri ◽

Ana Pina ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Group Method ◽

Japanese Plum ◽

Pair Group ◽

Prunus Salicina ◽

Wide Range ◽

High Level ◽

Informative Content

Japanese plum (Prunus salicina Lindl.) is widely distributed in temperate zones across the world. Since its introduction to USA in the late 19th century, this species has been hybridized with up to 15 different diploid Prunus species. This high level of introgression has resulted in a wide range of traits and agronomic behaviors among currently grown cultivars. In this work, 161 Japanese plum-type accessions were genotyped using a set of eight Simple Sequence Repeats (SSR) markers to assess the current genetic diversity and population structure. A total of 104 alleles were detected, with an average of 13 alleles per locus. The overall Polymorphic Informative Content (PIC) value of SSR markers was 0.75, which indicates that these SSR markers are highly polymorphic. The Unweighted Pair Group Method with Arithmetic (UPGMA) dendrogram and the seven groups inferred by Discriminant Analysis of Principal Components (DAPC) revealed a strong correlation of the population structure to the parentage background of the accessions, supported by a moderate but highly significant genetic differentiation. The results reported herein provide useful information for breeders and for the preservation of germplasm resources.

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Exploiting an oil palm EST database for the development of gene-derived SSR markers and their exploitation for assessment of genetic diversity

Biologia ◽

10.2478/s11756-008-0041-z ◽

2008 ◽

Vol 63 (2) ◽

Cited By ~ 36

Author(s):

Rajinder Singh ◽

Noorhariza Zaki ◽

Ngoot-Chin Ting ◽

Rozana Rosli ◽

Soon-Guan Tan ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Oil Palm ◽

Polymorphic Information Content ◽

Strong Association ◽

Geographic Location ◽

Group Method ◽

Pair Group ◽

High Level ◽

Nucleotide Repeats

AbstractA total of 5,521 expressed sequence tags (ESTs) from oil palm were used to search for type and frequency of simple sequence repeat (SSR) markers. Dimeric repeat motifs appeared to be the most abundant, followed by tri-nucleotide repeats. Redundancy was eliminated in the original EST set, resulting in 145 SSRs in 136 unique ESTs (114 singletons and 22 clusters). Primers were designed for 94 (69.1%) of the unique ESTs (consisting of 14 consensus and 80 singletons). Primers for 10 EST-SSRs were developed and used to evaluate the genetic diversity of 76 accessions of oil palm originating from seven countries in Africa, and the standard Deli dura population. The average number of observed and effective alleles was 2.56 and 1.84, respectively. The EST-SSR markers were found to be polymorphic with a mean polymorphic information content value of 0.53. Genetic differentiation (F ST) among the populations studied was 0.2492 indicating high level of genetic divergence. Moreover, the UPGMA (unweighted pair-group method with arithmetic mean) analysis revealed a strong association between genetic distance and geographic location of the populations studied. The germplasm materials exhibited higher diversity than Deli dura, indicating their potential usefulness in oil palm improvement programmes. The study also revealed that the populations from Nigeria, Congo and Cameroon showed the highest diversity among the germplasm evaluated in this study. The EST-SSRs further demonstrated their worth as a new source of polymorphic markers for phylogenetic analysis, since a high percentage of the markers showed transferability across species and palm taxa.

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