Identification of an Allelic Variant of the CsOr Gene Controlling Fruit Endocarp Color in Cucumber (Cucumis sativus L.) Using Genotyping-By-Sequencing (GBS) and Whole-Genome Sequencing.

Jeong-Gu Kim,Se-Young Lee,Hea-Young Lee,Hemasundar Alavilli,Kihwan Song,D. S. Kishor,Byoung-Cheorl Kang,Chae-Rin You

doi:10.3389/fpls.2021.802864

Abstract

The cucumber is a major vegetable crop around the world. Fruit flesh color is an important quality trait in cucumber and flesh color mainly depends on the relative content of β-carotene in the fruits. The β-carotene serves as a precursor of vitamin A, which has dietary benefits for human health. Cucumbers with orange flesh contain a higher amount of β-carotene than white fruit flesh. Therefore, development of orange-fleshed cucumber varieties is gaining attention for improved nutritional benefits. In this study, we performed genotyping-by-sequencing (GBS) based on genetic mapping and whole-genome sequencing to identify the orange endocarp color gene in the cucumber breeding line, CS-B. Genetic mapping, genetic sequencing, and genetic segregation analyses showed that a single recessive gene (CsaV3_6G040750) encodes a chaperone DnaJ protein (DnaJ) protein at the Cucumis sativus(CsOr) locus was responsible for the orange endocarp phenotype in the CS-B line. The Or gene harbored point mutations T13G and T17C in the first exon of the coding region, resulting in serine to alanine at position 13 and isoleucine to threonine at position 17, respectively. CS-B line displayed increased β-carotene content in the endocarp tissue, corresponding to elevated expression of CsOr gene at fruit developmental stages. Identifying novel missense mutations in the CsOr gene could provide new insights into the role of Or mechanism of action for orange fruit flesh in cucumber and serve as a valuable resource for developing β-carotene-rich cucumbers varieties with increased nutritional benefits.

Highlights

Cucumber (Cucumis sativus L., 2n = 14) is a major vegetable crop in the Cucurbitaceae family with economic and nutritional importance
Endocarp of the F1 derived from a cross between CS-B and CS-A and CS-A and CS-B was categorized as white (Figure 1A), while the fruits of BC1F1s derived from a cross between F1 (CS-A and CS-B) and CS-A demonstrated a white endocarp (Figure 1D)
F2 plants derived from a cross between CS-A and CS-B have white endocarp in 144 plants, whereas 62 plants showed the orange endocarp and segregated in a 3:1 ratio, suggesting that a single recessive gene was responsible for orange color endocarp phenotype in the CS-B line (Figure 1C and Table 1)

Summary

Introduction

Cucumber (Cucumis sativus L., 2n = 14) is a major vegetable crop in the Cucurbitaceae family with economic and nutritional importance. Cucumis sativus is native to India and was domesticated around 3,000 years ago and has extended its geographical distribution (Naegele and Wehner, 2017). Cucumbers are typically grown for fruits and are consumed fresh or as processed pickles across the globe. Cucumber ranked 3rd with an annual global production of 87,805,086 tons in an area of 2,231,402 ha (FAOSTAT, 2019) among the vegetable crops. China is the leading producer of cucumber, accounting for 70% of global production with an annual output of 54,315,900 tons, followed by Turkey, Iran, and Russia (Naegele and Wehner, 2017)

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