Analysis of Genetic Diversity and Population Structure in Sophora japonica Linn. in China With Newly Developed SSR Markers

Shu, Wen-Jiang; Tang, Jialei; Chen, Zongyou; Jiang, Yao; Wang, Zhengfeng; Xiao, Wei

doi:10.1007/s11105-019-01141-w

Cited by 5 publications

(3 citation statements)

References 38 publications

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“…HWE analysis showed that 10 loci (AM4, AM6, AM8, AM12, AM13, AM42, AM43, AM44, AM45, and AM49) significantly deviated from HWE (P < 0.05), and the remaining 13 loci (AM1, AM7, AM9, AM17, AM27, AM29, AM36, AM40, AM41, AM65, AM89, AM94, and AM99) were in accordance with HWE (Table 2). Micro-checker analysis showed that null alleles frequencies were lower than 0.2 for each locus, indicating these HWE deviations may be caused by anthropic selection and short-cloning history in cultivated rather than null alleles [12,21].…”

Section: Resultsmentioning

confidence: 95%

Development of 23 novel microsatellite markers of Amomum tsao-ko (Zingiberaceae) based on restriction-site-associated DNA sequencing

Zhang

et al. 2021

Mol Biol Rep

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Amomum tsao-ko (Zingiberaceae) is a traditional Chinese medicine and condiment, and an important economic crop in the tropical forest of southwest China. However, few simple sequence repeat (SSR) markers are available in A. tsao-ko, which is hindering genetic research in this species. The aim of this study was to develop and characterize microsatellite markers for A. tsao-ko using restriction-site-associated DNA sequencing. A total of 115,482 microsatellites were identified using MISA software, and 13,411 SSR primer pairs were designed. 100 pairs of SSR primers were selected at random and used to evaluate polymorphisms among 4 A. tsao-ko samples. Finally, 23 pairs of SSR primers with clear bands and obvious polymorphism were selected for genetic diversity analysis of 72 A. tsao-ko accessions. The number of alleles and effective number of alleles per locus ranged from 2 to 6 and from 1.315 to 3.776, respectively. The observed heterozygosity ranged from 0.208 to 0.779, and the expected heterozygosity was from 0.239 to 0.735. The average values of the polymorphic information content were 0.454. Hardy-Weinberg equilibrium (HWE) analysis showed that 10 loci significantly deviated from HWE (P < 0.05). The pairwise F ST and genetic distance values revealed low levels of genetic differentiation and high genetic similarity among six A. tsao-ko populations. These microsatellite markers developed will provide a valuable tool for further germplasm characterization, genetic diversity, and breeding studies in A. tsao-ko.

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Section: Resultsmentioning

confidence: 95%

Development of 23 novel microsatellite markers of Amomum tsao-ko (Zingiberaceae) based on restriction-site-associated DNA sequencing

Zhang

et al. 2021

Mol Biol Rep

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“…alopecuroides , which provided a relative full assessment of the genetic diversity and population structure of this species for the first time at population level. Compared with other species in the genus Sophora [42, 43], such as S . fulvida (H o = 0.44, H e = 0.60), S .…”

Section: Discussionmentioning

confidence: 99%

The genetic diversity and population structure of Sophora alopecuroides (Faboideae) as determined by microsatellite markers developed from transcriptome

Yuan

Zhou

et al. 2019

PLoS ONE

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Sophora alopecuroides (Faboideae) is an endemic species, mainly distributed in northwest China. However, the limited molecular markers range for this species hinders breeding and genetic studies. A total of 20,324 simple sequence repeat (SSR) markers were identified from 118,197 assembled transcripts and 18 highly polymorphic SSR markers were used to explore the genetic diversity and population structure of S. alopecuroides from 23 different geographical populations. A relatively low genetic diversity was found in S. alopecuroides based on mean values of the number of effective alleles (Ne = 1.81), expected heterozygosity (He = 0.39) and observed heterozygosity (Ho = 0.55). The results of AMOVA indicated higher levels of variation within populations than between populations. Bayesian-based cluster analysis, principal coordinates analysis and Neighbor-Joining phylogeny analysis roughly divided all genotypes into four major groups with some admixtures. Meanwhile, geographic barriers would have restricted gene flow between the northern and southern regions (separated by Tianshan Mountains), wherein the two relatively ancestral and independent clusters of S. alopecuroides occur. History trade and migration along the Silk Road would together have promoted the spread of S. alopecuroides from the western to the eastern regions of the northwest plateau in China, resulting in the current genetic diversity and population structure. The transcriptomic SSR markers provide a valuable resource for understanding the genetic diversity and population structure of S. alopecuroides, and will assist effective conservation management.

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“…Semiothisa cinerearia (Bremer et Gray), which belongs to the subfamily Ennominae (Lepidoptera: Geometridae), is a forestry pest that attacks Sophora japonica. S. japonica, which is native to China and known as the Chinese scholar tree, widely cultivated in urban greenbelts in China [23,24]. In recent years, Chinese scholar trees have been severely damaged by S. cinerearia in northern China.…”

Section: Introductionmentioning

confidence: 99%

The Female-Biased General Odorant Binding Protein 2 of Semiothisa cinerearia Displays Binding Affinity for Biologically Active Host Plant Volatiles

Tu,

Wang,

Yang

et al. 2024

Biology

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Herbivorous insects rely on volatile chemical cues from host plants to locate food sources and oviposition sites. General odorant binding proteins (GOBPs) are believed to be involved in the detection of host plant volatiles. In the present study, one GOBP gene, ScinGOBP2, was cloned from the antennae of adult Semiothisa cinerearia. Reverse-transcription PCR and real-time quantitative PCR analysis revealed that the expression of ScinGOBP2 was strongly biased towards the female antennae. Fluorescence-based competitive binding assays revealed that 8 of the 27 host plant volatiles, including geranyl acetone, decanal, cis-3-hexenyl n-valerate, cis-3-hexenyl butyrate, 1-nonene, dipentene, α-pinene and β-pinene, bound to ScinGOBP2 (KD = 2.21–14.94 μM). The electrical activities of all eight ScinGOBP2 ligands were confirmed using electroantennography. Furthermore, oviposition preference experiments showed that eight host volatiles, such as decanal, cis-3-hexenyl n-valerate, cis-3-hexenyl butyrate, and α-pinene, had an attractive effect on female S. cinerearia, whereas geranyl acetone, 1-nonene, β-pinene, and dipentene inhibited oviposition in females. Consequently, it can be postulated that ScinGOBP2 may be implicated in the perception of host plant volatiles and that ScinGOBP2 ligands represent significant semiochemicals mediating the interactions between plants and S. cinerearia. This insight could facilitate the development of a chemical ecology-based approach for the management of S. cinerearia.

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Analysis of Genetic Diversity and Population Structure in Sophora japonica Linn. in China With Newly Developed SSR Markers

Cited by 5 publications

References 38 publications

Development of 23 novel microsatellite markers of Amomum tsao-ko (Zingiberaceae) based on restriction-site-associated DNA sequencing

Development of 23 novel microsatellite markers of Amomum tsao-ko (Zingiberaceae) based on restriction-site-associated DNA sequencing

The genetic diversity and population structure of Sophora alopecuroides (Faboideae) as determined by microsatellite markers developed from transcriptome

The Female-Biased General Odorant Binding Protein 2 of Semiothisa cinerearia Displays Binding Affinity for Biologically Active Host Plant Volatiles

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