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Dynamic and epistatic QTL mapping reveals the complex genetic architecture of waterlogging tolerance in chrysanthemum

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Abstract

Main conclusion

37 unconditional QTLs, 51 conditional QTLs and considerable epistatic QTLs were detected for waterlogging tolerance, and six favourable combinations were selected accelerating the possible application of MAS in chrysanthemum breeding.

Chrysanthemum is seriously impacted by soil waterlogging. To determine the genetic characteristics of waterlogging tolerance (WAT) in chrysanthemum, a population of 162 F1 lines was used to construct a genetic map to identify the dynamic and epistatic quantitative trait loci (QTLs) for four WAT traits: wilting index (WI), dead leaf ratio (DLR), chlorosis score (Score) and membership function value of waterlogging (MFVW). The h 2B for the WAT traits ranged from 0.49 to 0.64, and transgressive segregation was observed in both directions. A total of 37 unconditional consensus QTLs with 5.81–18.21% phenotypic variation explanation (PVE) and 51 conditional consensus QTLs with 5.90–24.56% PVE were detected. Interestingly, three unconditional consensus QTLs were consistently identified across different stages, whereas no conditional consensus QTLs were consistently expressed. In addition, considerable epistatic QTLs, all with PVE values ranging from 0.01 to 8.87%, were detected by a joint analysis of WAT phenotypes. These results illustrated that the QTLs (genes) controlling WAT were environmentally dependent and selectively expressed at different times and indicated that both additive and epistatic effects underlie the inheritance of WAT in chrysanthemum. The findings of the current study provide insights into the complex genetic architecture of WAT, and the identification of favourable alleles represents an important step towards the application of molecular marker-assisted selection (MAS) and QTL pyramiding in chrysanthemum WAT breeding programmes.

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Abbreviations

DLR:

Dead leaf ratio

gSSR:

Genomic simple sequence repeat

LG:

Linkage group

LOD:

Logarithm of odds

MAS:

Marker assisted selection

MB:

Monalisa cv

MFVW:

Membership function value of waterlogging

PVE:

Phenotypic variance explained

QTL:

Quantitative trait loci

Score:

Chlorosis score

SRAP:

Sequence-related amplified polymorphism

WAT:

Waterlogging tolerance

WI:

Wilting index

XF:

Nannong Xuefeng cv

XM:

XF and MB population

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Acknowledgements

This work was financially supported by the National Science Fund for Distinguished Young Scholars (31425022), Key Projects of National Natural Science Foundation of China (31730081), Fund for Independent Innovation of Agricultural Sciences in Jiangsu Province [CX (16) 1025], Special Fund for Agroscientific Research in the Public Interest (201403039), “948” Project of Ministry of Agriculture (2016-X18), and Fundamental Research Funds for the Central Universities (KYRC201601, KYCYL201501).

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  1. Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, People’s Republic of China

    Jiangshuo Su, Xincheng Yang, Fei Zhang, Shaofang Wu, Siyi Xiong, Liming Shi, Zhiyong Guan, Weimin Fang & Fadi Chen

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  1. Jiangshuo Su
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425_2017_2833_MOESM1_ESM.tif

Fig. S1 The daily mean temperature (a) and relative humidity (b) at the four measured stages in the two environments (TIFF 2847 kb)

425_2017_2833_MOESM2_ESM.tif

Fig. S2 A genetic linkage map for chrysanthemum XF based on testcross markers at an LOD threshold of 4.0. The cumulative genetic distances (cM) are indicated on the left side of each LG, and the names of the markers are on the right side. Markers with red colour are gSSR, and the prefix * or ** indicates a segregation distortion at P < 0.05 and P < 0.01, respectively (TIFF 10204 kb)

425_2017_2833_MOESM3_ESM.tif

Fig. S3 A genetic linkage map for chrysanthemum MB based on testcross markers at an LOD threshold of 4.0. The cumulative genetic distances (cM) are indicated on the left side of each LG, and the names of the markers are on the right side. Markers with red colour are gSSR, and the prefix * or ** indicates a segregation distortion at P < 0.05 and P < 0.01, respectively (TIFF 13472 kb)

425_2017_2833_MOESM4_ESM.tif

Fig. S4 MFVW values of XF, MB, and the seven selected F1 lines at four stages in environments E1 (a) and E2 (b) (TIFF 2821 kb)

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Su, J., Yang, X., Zhang, F. et al. Dynamic and epistatic QTL mapping reveals the complex genetic architecture of waterlogging tolerance in chrysanthemum. Planta 247, 899–924 (2018). https://doi.org/10.1007/s00425-017-2833-2

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