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. 2021;68(6):2655-2667.
doi: 10.1007/s10722-021-01204-6. Epub 2021 May 20.

Assessment of genetic diversity in Amomum tsao-ko Crevost & Lemarié, an important medicine food homologous crop from Southwest China using SRAP and ISSR markers

Mengli Ma  1 , Tiantao Wang  1 , Bingyue Lu  1
Affiliations

Assessment of genetic diversity in Amomum tsao-ko Crevost & Lemarié, an important medicine food homologous crop from Southwest China using SRAP and ISSR markers

Mengli Ma et al. Genet Resour Crop Evol. 2021.

Abstract

Amomum tsao-ko Crevost & Lemarié is an important crop that has been widely used in traditional Chinese medicine and daily diets for a long time. In this study, the genetic diversity and relationships of eight cultivated populations of A. tsao-ko grown in Southwest China were examined using sequence-related amplified polymorphism (SRAP) and inter-simple sequence repeat (ISSR) markers. The results showed that 139 (99.29%) of 140 and 185 (99.46%) of 186 bands were polymorphic by SRAP and ISSR primers amplification, respectively. The polymorphic information content of detected bands were 0.270 (SRAP) and 0.232 (ISSR), respectively. The average Nei's gene diversity (H = 0.217) and Shannon's information index (I = 0.348) at the species level generated by SRAP primer were higher than those by ISSR analysis (H = 0.158, I = 0.272). Genetic differentiation coefficients and molecular variance analysis (AMOVA) indicated that the genetic variance of A. tsao-ko mainly occurred within populations rather than among populations. The high genetic identity among populations was revealed by SRAP (0.937) and ISSR (0.963). Using UPGMA cluster analysis, principal coordinate analysis, and population structure analysis, the accessions were categorized into two major groups. Overall, results obtained here will be useful for A. tsao-ko germplasm characterization, conservation, and utilization.

Keywords: Amomum tsao-ko; Genetic variance; Molecular markers; Population structure.

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Conflict of interest statement

Conflict of interestThe authors declare no conflict of interest.

Figures

Fig. 1
Fig. 1
Map of A. tsao-ko samples collection sites. PB, Pingbian population; JP, Jinping population; YY, Yuanyang population; LVC, Lvchun population; YX, Yunxian population; LC, Lancang population; BS, Baoshan population; DH, Dehong population
Fig. 2
Fig. 2
Electrophoretic profiles of genomic DNA amplification products using SRAP primer Me1/Em12 (a), Me2Em12 (b) and ISSR primer UBC880 (c), UBC888 (d). Lane M indicated DNA Marker (200, 400, 700, 1000, 1500, 2000 bp). Lane 1–48 indicated partial A. tsao-ko accessions: JP8, JP48, JP55, JP59, JP64, JP84, JP91, JP103, JP108, JP109, JP118, JP119, JP128, YY3, YY5, YY9, YY14, YY18, YY22, YY32, YY36, YY44, YY45, YY47, YY48, LVC2, LVC5, LVC12, LVC21, LVC25, LVC28, LVC34, LVC41, LVC44, LVC49, LVC50, PB1, PB2, PB19, PB21, PB30, PB31, PB41, PB45, PB48, LC1, LC2 and LC3
Fig. 3
Fig. 3
UPGMA cluster of 91 A. tsao-ko accessions based on SRAP (a), ISSR (b) and combined SRAP  + SSR (c) markers
Fig. 4
Fig. 4
Principal coordinates analysis (PCA) of the 91 A. tsao-ko accessions based on SRAP  + SSR markers
Fig. 5
Fig. 5
Graphical representation of population structure using STRUCTURE 2.3.4 and Structure Harvester v6.0 program, a Evanno table output, b the median and variance of the estimated probability value for each K value, c Population structure of 91 A. tsao-ko accessions
See this image and copyright information in PMC

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