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Molecular mapping reveals structural rearrangements and quantitative trait loci underlying traits with local adaptation in semi-wild Xishuangbanna cucumber (Cucumis sativus L. var. xishuangbannanesis Qi et Yuan)

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Comparative genetic mapping revealed the origin of Xishuangbanna cucumber through diversification selection after domestication. QTL mapping provided insights into the genetic basis of traits under diversification selection during crop evolution.

Abstract

The Xishuangbanna cucumber, Cucumis sativus L. var. xishuangbannanesis Qi et Yuan (XIS), is a semi-wild landrace from the tropical southwest China with some unique traits that are very useful for cucumber breeding, such as tolerance to low light, large fruit size, heavy fruit weight, and orange flesh color in mature fruits. In this study, using 124 recombinant inbred lines (RILs) derived from the cross of the XIS cucumber with a cultivated cucumber inbred line, we developed a linkage map with 269 microsatellite (or simple sequence repeat) markers which covered 705.9 cM in seven linkage groups. Comparative analysis of orders of common marker loci or marker-anchored draft genome scaffolds among the wild (C. sativus var. hardwickii), semi-wild, and cultivated cucumber genetic maps revealed that the XIS cucumber shares major chromosomal rearrangements in chromosomes 4, 5, and 7 between the wild and cultivated cucumbers suggesting that the XIS cucumber originated through diversifying selection after cucumber domestication. Several XIS-specific minor structural changes were identified in chromosomes 1 and 6. QTL mapping with the 124 RILs in four environments identified 13 QTLs for domestication and diversifying selection-related traits including 2 for first female flowering time (fft1.1, fft6.1), 5 for mature fruit length (fl1.1, fl3.1, fl4.1, fl6.1, and fl7.1), 3 for fruit diameter (fd1.1, fd4.1, and fd6.1), and 3 for fruit weight (fw2.1, fw4.1, and fw6.1). Six of the 12 QTLs were consistently detected in all four environments. Among the 13 QTLs, fft1.1, fl1.1, fl3.1, fl7.1, fd4.1, and fw6.1 were major-effect QTLs for respective traits with each explaining at least 10 % of the observed phenotypic variations. Results from this study provide insights into the cytological and genetic basis of crop evolution leading to the XIS cucumber. The molecular markers associated with the QTLs should be useful in exploring the XIS cucumber genetic resources for cucumber breeding.

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Acknowledgments

The authors thank Kristin Haider for technical assistance. KB’s work in YW’s laboratory was partially funded by the China Scholarship Council. This research was supported by the US Department of Agriculture Current Research Information System Project 3655-21000-048-00D and a US Department of Agriculture Specialty Crop Research Initiative grant (project number 2011-51181-30661) to Y.W. Work pertinent to this project in JC Lab was supported by the Natural Science Foundation of China (30972007 and 31272174) and the ‘973’ Program (2012CB113904) from the National Basic Research Program of China and ‘863’ project (2012AA100102).

Conflict of interest

The authors declare no conflict of interest.

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Authors and Affiliations

  1. Horticulture College, Nanjing Agricultural University, Nanjing, 210095, China

    Kailiang Bo, Zheng Ma & Jinfeng Chen

  2. Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA

    Kailiang Bo & Yiqun Weng

  3. Vegetable Crops Research Unit, USDA-ARS, 1575 Linden Drive, Madison, WI, 53706, USA

    Yiqun Weng

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  1. Kailiang Bo
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  2. Zheng Ma
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  3. Jinfeng Chen
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Correspondence to Jinfeng Chen or Yiqun Weng.

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Communicated by Alan H. Schulman.

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122_2014_2410_MOESM1_ESM.pdf

Table S1 Major statistics of the CC3 × SWCC8 RIL linkage map developed in the present study.Table S2 Information of 269 markers placed on the CC3 × SWCC8 RIL genetic map, QTL and melon fruit shape homolog locations.Fig. S1 Alignments of marker loci in seven cucumber chromosomes based on comparison of the semi-wild CC3 × SWCC8 RIL genetic map (this study, center), the cultivated Gy14 × 9930 F2 map (Yang et al. 2012), as well as the wild cucumber Gy14 × PI 183967 (C. s. var. hardwickii) RIL map (Ren et al. 2009). Marker loci connected with red dotted lines are shared across three maps; green and blue lines connect shared markers between the Gy14 × 9930 F2 and the CC3 × SWCC8 RIL maps, as well as between the CC3 × SWCC8 RIL and the Gy14 × PI 183967 RIL maps, respectively. LG = linkage group.Fig. S2 Frequency distribution of first female flowering time (FFT), fruit length (FL), fruit diameter (FD), and fruit weight (FW) among 436 CC3 × SWCC8 F2 plants in WI2012H experiment.Fig. S3 Whole genome view of QTL locations for first female flowering time (FFT, A), fruit length (FL, B), fruit diameter (FD, C), fruit length to diameter ratio (L/D, D), and fruit weight (FW, E) detected in four experiments (NJ2009F, NJ2012S, WI2012H, WI 2013H). LOD profile screen snapshots were taken from WinQTL Cartographer 2.5. For each trait, the X axis represents linkage map of seven chromosomes, and the Y axis is LOD scores; the horizontal line represents LOD threshold obtained with 1,000 permutation tests (P = 0.05). To the right of the global view is the LOD profile of the major-effect QTL for FFT at chromosome 1 (fft1.1, A1), FL at chromosome 1 (fl1.1, B1), FD at chromosome 1 (fd1.1, C1), L/D at chromosome 1 (fld1.1, D1), and FW at chromosome 6 (fw6.1, E1).Fig. S4 Frequency distribution of 394 SWCC8 × CC3 F2 plants from WI2013H field trial based on fruit length (green), and genotypes (AA: red; AB: blue; BB: black) at the marker SSR12331 locus which was closely linked with the major-effect QTL fl1.1 for fruit length. Plants with shorter fruits were enriched with the B allele from SWCC8 while those with longer fruits had higher frequency of the A allele from CC3. (PDF 2847 kb)

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Bo, K., Ma, Z., Chen, J. et al. Molecular mapping reveals structural rearrangements and quantitative trait loci underlying traits with local adaptation in semi-wild Xishuangbanna cucumber (Cucumis sativus L. var. xishuangbannanesis Qi et Yuan). Theor Appl Genet 128, 25–39 (2015). https://doi.org/10.1007/s00122-014-2410-z

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