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Title: 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)

Author
item BO, KAILIANG - Nanjing Agricultural University
item MA, ZHENG - Nanjing Agricultural University
item CHEN, JINFENG - Nanjing Agricultural University
item Weng, Yiqun

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/1/2014
Publication Date: 10/31/2014
Citation: Bo, K., Ma, Z., Chen, J., Weng, Y. 2014. 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). Theoretical and Applied Genetics. 128(1):25-39.

Interpretive Summary: 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 such as tolerance to low light, large fruit size and heavy fruit weight, as well as orange flesh color in mature fruits that are very useful for cucumber breeding. 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 for the XIS cucumber with 269 SSR marker loci that 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, semi-wild, and cultivated cucumber genetic maps revealed that the XIS cucumber shares the major chromosomal rearrangements in chromosomes 4, 5 and 7 between the wild and cultivated cucumbers suggesting the origin of the XIS cucumber through diversification selection after cucumber domestication. Several XIS-specific minor structural changes were identified in chromosomes 1 and 6. In a QTL mapping study with the 124 RILs in four environments, we identified 12 QTLs with 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 2 for fruit weight (fw4.1, and fw6.1). Six of the 12 QTLs were consistently detected in all four environments, and only fw4.1 was identified in one environment. Among the 12 QTLs, fft1.1, fl1.1, fl3.1, fl7.1, fd4.1, and fw6.1 were major effect QTLs for respective traits that could explain at least 10% phenotypic variations each. Results from this study provide important information on the cytological and genetic basis of crop evolution leading to the XIS cucumber. The molecular markers associated with the QTLs should be useful in using the genetic resources of XIS cucumber in cucumber breeding.

Technical Abstract: The Xishuangbanna cucumber (XIS) is a semi-wild landrace from the tropical southwest China with some unique traits such as tolerance to low light, large fruit size and heavy fruit weight, as well as orange flesh color in mature fruits that are very useful for cucumber breeding. In this study, we investigated the genetic differentiation of XIS cucumber with cultivated and wild cucumbers as well as the genetic basis of these unique traits in XIS cucumber. We used 124 recombinant inbred lines (RILs) derived from the cross of the XIS cucumber with a cultivated cucumber line and developed a linkage map with 269 molecular markers in seven linkage groups. Comparative analysis of orders of common markers revealed that the XIS cucumber shares the major chromosomal rearrangements in chromosomes 4, 5 and 7 between the wild and cultivated cucumbers suggesting the origin of the XIS cucumber through diversification 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 12 QTLs with 2 for first female flowering time, 5 for mature fruit length, 3 for fruit diameter, and 2 for fruit weight. Six of the 12 QTLs were consistently detected in all four environments. Among the 12 QTLs, six were major effect QTLs for respective traits that could explain at least 10% phenotypic variations each. Results from this study provide important information on the cytological and genetic basis of crop evolution leading to the XIS cucumber. The molecular markers associated with the QTLs should be useful in using the genetic resources of XIS cucumber in cucumber breeding.