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Genetic variation and association mapping of waterlogging tolerance in chrysanthemum

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Abstract

Main conclusion

Forty-five molecular markers were detected significantly associated with chrysanthemum’ waterlogging tolerance, and four favorable parental lines were identified as potential donors for improving waterlogging tolerance in chrysanthemum.

The productivity of chrysanthemum is downgraded by waterlogging soils, which has driven a search for germplasm showing an enhanced level of waterlogging tolerance (WT). As yet little is known regarding the mode of inheritance of WT in chrysanthemum. The study set out to characterize the extent of genetic variation for WT represented in a collection of one hundred chrysanthemum accessions by testing them under both greenhouse and field conditions. A membership function value of waterlogging (MFVW), which integrated a wilting index, a chlorosis score and the proportion of dead leaf in waterlogged plants, was used as a measure of WT. The variation for MFVW among plants grown in the greenhouse (two experiments) was generally higher than that generated in field-grown (one experiment) plants. The MFVW broad sense heritability was 0.82, and the phenotypic coefficient of variation (31.8 %) was larger than the genetic one (28.8 %). Association mapping (AM) identified 45 markers related to WT: 25 by applying the general linear model (GLM) + principal component (PC) model, 16 by applying the mixed linear model (MLM), 31 by applying the MLM + Q matrix model and 12 by applying the MLM + PC model. Of the associated markers, eight and two were predictive in two and three experiments within all models, respectively; the proportion of the phenotypic variance explained by the eight associations ranged from 6.3 to 16.4 %. On the basis of their harboring all four of the leading markers E2M16-2, SSR150-6, E19M16-1 and E10M10-12, the varieties ‘Nannong Xuefeng’, ‘Qx097’, ‘Nannong Xunzhang’ and ‘Finch’ were identified as potential donors for future improvement of WT in chrysanthemum.

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Abbreviations

AM:

Association mapping

GLM:

General linear model

MFVW:

Membership function value of waterlogging

MLM:

Mixed linear model

PC:

Principal component

SSR:

Simple sequence repeats

WT:

Waterlogging tolerance

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Acknowledgments

The authors are grateful to anonymous reviewers and editor for their constructive comments and suggestion that significantly improved the presentation of this manuscript. This work was supported by the grant from the National Natural Science Foundation of China (Grant nos. 31425022 and 31272196).

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Authors and Affiliations

  1. College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People’s Republic of China

    Jiangshuo Su, Fei Zhang, Pirui Li, Zhiyong Guan, Weimin Fang & Fadi Chen

  2. Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, Jiangsu, People’s Republic of China

    Pirui Li

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  1. Jiangshuo Su
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Correspondence to Fadi Chen.

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Electronic supplementary material

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Fig. S1 Frequency distribution of WT classification grades in each of the three experiments (TIFF 55 kb)

425_2016_2583_MOESM2_ESM.tif

Fig. S2 The phenotype of six of the entries in EXP.1. The images were taken after ten days of flooding. CK, non-stressed control; T, flooded plants (TIFF 1401 kb)

425_2016_2583_MOESM3_ESM.tif

Fig. S3 The structure of the germplasm panel (K = 2). a Means of log likelihoods and their standard deviations. b △K values as a function of K. c each bar represents a single accession, and the colored portions of the bar represents the proportional contribution of each of the two subpopulations to a given entry. Entries with a > 60 % contribution were classified as either Pop1 (green) or Pop 2 (red) (TIFF 340 kb)

Fig. S4 The distribution of pair-wise kinship coefficients in the AM germplasm panel (TIFF 66 kb)

425_2016_2583_MOESM5_ESM.tif

Fig. S5 Quantile–quantile (Q–Q) probability plots for wilting index (WI), chlorosis Score and proportion of dead leaf (PDL) obtained from the application of six AM models. The models tested were GLM (a), GLM + Q (b), GLM + PC (c), MLM (d), MLM + Q (e) and MLM + PC (f). Each dot represents a marker (TIFF 1925 kb)

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Su, J., Zhang, F., Li, P. et al. Genetic variation and association mapping of waterlogging tolerance in chrysanthemum. Planta 244, 1241–1252 (2016). https://doi.org/10.1007/s00425-016-2583-6

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