Genetic variation and association mapping in the F2 population of the Perilla crop (Perilla frutescens L.) using new developed Perilla SSR markers

ABSTRACTMolecular Marker-based Selection on F2 Progeny for Development of Promising Rice Lines Resistant to Brown PlanthopperBrown planthopper (BPH) is the major insect pest of rice and accounts for significant yield loss. This experiment was aimed to develop BC1F1 and F3 brown planthopper resistant rice lines. Selection on the basis of SSR markers can be done by using two polymorphic SSR markers, i.e., RM586 dan RM8213, which screened from eight SSR markers for BPH resistant. Sixty-three F2 genotypes from IP-1 (derived from IR-64 x PTB-33) population and twenty F2 genotypes from PP-11 (derived from Pandan Wangi x PTB-33) population were selected and will be used for further research by selfed and backcrossed to recipient parents. Chi-squares test for segregation of DNA bands in F2 generation showed that RM8213 fitted with 1:2:1 Mendelian ratio for controlling photosynthetic rates and trichomes length in IP-1 population. This information could be used in programs to develop a durable brown planthopper resistant rice cultivar.Keywords: BPH, F2 population, Moleculer marker, SSRABSTRAKWereng coklat merupakan salah satu hama utama pada tanaman padi yang mampu menurunkan produksi padi secara nyata. Penelitian ini bertujuan untuk memperoleh galur-galur padi F2 yang memiliki marka-marka yang berasosisasi dengan ketahanannya terhadap wereng coklat. Seleksi pada galur padi F2 hasil persilangan telah dilakukan melalui teknik marka molekuler Simple Sequence Repeat (SSR) menggunakan dua marka SSR yang menunjukkan polimorphisme yaitu RM586 dan RM8213 dari delapan marka yang diskrining. Sebanyak 63 genotip dari populasi IP-1 (hasil persilangan IR-64 x PTB-33) dan 20 genotip dari populasi PP-11 (hasil persilangan Pandan Wangi x PTB-33) untuk disilangkan sendiri maupun disilang balik dengan tetua recipient. Selain itu, hasil analisis Chi-Kuadrat untuk segregasi pita DNA menunjukkan bahwa primer RM8213 memiliki rasio 1:2:1 (dominasi tidak sempurna) dalam mengontrol karakter laju fotosintesis dan panjang trikoma terhadap wereng coklat pada populasi IP-1. Informasi yang diperoleh dari penelitian ini nantinya dapat digunakan untuk program perakitan kultivar padi tahan wereng coklat yang durable.Kata Kunci: Marka molekuler, Populasi F2, SSR, Wereng coklat

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Dissection of the genetic basis of oil content in Chinese peanut cultivars through association mapping

10.21203/rs.3.rs-17113/v2 ◽

2020 ◽

Author(s):

Nian Liu ◽

Li Huang ◽

Weigang Chen ◽

Bei Wu ◽

Manish K. Pandey ◽

...

Keyword(s):

Association Mapping ◽

Ssr Markers ◽

Oil Content ◽

Genetic Basis ◽

Principal Component ◽

Primary Sources ◽

Phenotypic Variance ◽

Mapping Panel ◽

Stable Association ◽

Faster Development

Abstract Background: Peanut is one of the primary sources for vegetable oil worldwide, and enhancing oil content is the main objective in several peanut breeding programs of the world. Tightly linked markers are required for faster development of high oil content peanut varieties through genomics-assisted breeding (GAB), and association mapping is one of the promising approaches for discovery of such associated markers. Results: An association mapping panel consisting of 292 peanut varieties extensively distributed in China was phenotyped for oil content and genotyped with 583 polymorphic SSR markers. These markers amplified 3663 alleles with an average of 6.28 alleles per locus. The structure, phylogenetic relationship, and principal component analysis (PCA) indicated two subgroups majorly differentiating based on geographic regions. Genome-wide association analysis identified 12 associated markers including one (AGGS1014_2) highly stable association controlling up to 9.94% phenotypic variance explained (PVE) across multiple environments. Interestingly, the frequency of the favorable alleles for 12 associated markers showed a geographic difference. Two associated markers (AGGS1014_2 and AHGS0798) with 6.90-9.94% PVE were verified to enhance oil content in an independent RIL population and also indicated selection during the breeding program. Conclusion: This study provided insights into the genetic basis of oil content in peanut and verified highly associated two SSR markers to facilitate marker-assisted selection for developing high-oil content breeding peanut varieties.

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Mapping Some Seed Quality Traits in Bread Wheat (Triticum aestivum L.) by Association Mapping Using SSR Markers

Journal of Applied Biotechnology Reports ◽

10.29252/jabr.05.03.02 ◽

2018 ◽

Vol 5 (3) ◽

pp. 92-99 ◽

Cited By ~ 1

Author(s):

Reza Mir Drikvand ◽

Goodarz Najafian ◽

Mohammad Reza Bihamta ◽

Asa Ebrahimi

Keyword(s):

Triticum Aestivum ◽

Association Mapping ◽

Bread Wheat ◽

Ssr Markers ◽

Seed Quality ◽

Triticum Aestivum L ◽

Quality Traits ◽

Seed Quality Traits

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Analysis of Population Structure and Association Mapping among Popcorn Inbred Lines using SSR markers

Korean Journal of Breeding Science ◽

10.9787/kjbs.2013.45.4.358 ◽

2013 ◽

Vol 45 (4) ◽

pp. 358-368 ◽

Cited By ~ 1

Author(s):

Jin-Sun Jang ◽

Eun-Ha Chang ◽

Kyu Jin Sa ◽

Byeong Wan Kim ◽

Jong-Hwa Kim ◽

...

Keyword(s):

Population Structure ◽

Association Mapping ◽

Ssr Markers ◽

Inbred Lines

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Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics ofPulsatilla patenspopulations

PeerJ ◽

10.7717/peerj.2504 ◽

2016 ◽

Vol 4 ◽

pp. e2504 ◽

Cited By ~ 1

Author(s):

Katarzyna Bilska ◽

Monika Szczecińska

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Conservation Genetics ◽

Ssr Markers ◽

Full Range ◽

Mantel Test ◽

Evolutionary Potential ◽

Functional Variation ◽

Genetics Research ◽

Outlier Loci

BackgroundResearch into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation inPulsatilla patenspopulations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction).MethodsThe experiment was conducted on 14 Polish populations ofP. patensand threeP. patenspopulations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific toP. patensand three ISJ primers.ResultsSSR markers revealed a higher level of genetic variation than ISJ markers (He= 0.609,He= 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parametersFSTand ΦPTfor SSR (20%) and ΦPTfor ISJ (21%) markers was similar. Analysis conducted in theStructureprogram divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations ofP. patensfor ISJ markers, but not for SSR markers.ConclusionsThe results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs.

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