Identification of a candidate gene responsible for the G locus determining chartreuse bulb color in onion (Allium cepa L.) using bulked segregant RNA-Seq

Onions (Allium cepa L.) are one of the most consumed vegetable crops worldwide and are damaged by several fungal diseases in the field or during storage. Gray mold disease caused by the necrotrophic pathogens Botrytis cinerea and Botrytis squamosa is a disease that reduces the productivity and storage life in onions. However, it is difficult to control gray mold disease in onions by using physical and chemical methods. Breeding resistant onions against gray mold disease can reduce the damage caused by pathogens, reduce the labor required for control, and reduce environmental pollution caused by fungicides. However, onions have a large genome size (16Gb), making them difficult to analyze, and have a biennial cycle, resulting in a very long breeding period. Therefore, in this study, markers were developed to shorten the onion breeding period. First, random amplified polymorphic DNA (RAPD) was performed to confirm the genetic relationship between the gray mold disease-resistant and -susceptible lines through a dendrogram. In addition, the sequence characterized amplified region (SCAR)-OPAN1 marker to select resistant lines was developed using a polymorphic RAPD fragment. Second, the RNA-seq of the gray mold-resistant and -susceptible onion lines were analyzed using NGS technology. Using the RNA-seq results and DEG and GO analyses were performed, and the variants, such as SNPs and indels, were analyzed to develop a selectable marker for the resistant line. This study developed the SNP-3 HRM marker for selecting gray mold disease-resistant lines by using the SNPs present in the aldo-keto reductase (AKR) gene with high expression levels in these lines. The SCAR-OPAN1 and SNP-3 HRM markers developed in this study could be used to select gray mold disease-resistant onions in breeding programs to reduce the damage caused by gray mold disease.

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Transposition of a non-autonomous DNA transposon in the gene coding for a bHLH transcription factor results in a white bulb color of onions (Allium cepa L.)

Theoretical and Applied Genetics ◽

10.1007/s00122-019-03460-8 ◽

2019 ◽

Vol 133 (1) ◽

pp. 317-328 ◽

Cited By ~ 2

Author(s):

Changyeong Jo ◽

Sunggil Kim

Keyword(s):

Transcription Factor ◽

Allium Cepa ◽

Bhlh Transcription Factor ◽

Dna Transposon ◽

Gene Coding ◽

Allium Cepa L ◽

Bulb Color

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Construction of a linkage map flanking the I locus controlling dominant white bulb color and analysis of differentially expressed genes between dominant white and red bulbs in onion (Allium cepa L.)

Euphytica ◽

10.1007/s10681-020-02638-2 ◽

2020 ◽

Vol 216 (6) ◽

Cited By ~ 1

Author(s):

Inho Seo ◽

Ju-Gyeong Kim ◽

Jae-Hak Moon ◽

Sunggil Kim

Keyword(s):

Linkage Map ◽

Differentially Expressed Genes ◽

Allium Cepa ◽

Differentially Expressed ◽

Allium Cepa L ◽

Bulb Color

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Metabolite profile of two Allium cepa L. aggregatum group cultivars by Nuclear Magnetic Resonance

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d220806 ◽

2021 ◽

Vol 22 (8) ◽

Author(s):

Fransiska Renita Anon Basundari ◽

Endang Sulistyaningsih ◽

Rudi Hari Murti ◽

Tri Rini Nuringtyas

Keyword(s):

Nuclear Magnetic Resonance ◽

Magnetic Resonance ◽

Allium Cepa ◽

Metabolite Profile ◽

Two Phase ◽

Allium Species ◽

Freeze Dried ◽

Allium Cepa L ◽

Bulb Color ◽

Nuclear Magnetic

Abstract. Basundari FRA, Sulistyaningsih E, Murti RH, Nuringtyas TR. 2021. Metabolite profile of two Allium cepa L. aggregatum group cultivars by Nuclear Magnetic Resonance. Biodiversitas 22: 3127-3135. Shallot, an Allium species with high economic value, is widely cultivated in Indonesia. The species includes numerous cultivars with unique characteristics, such as harvesting time, yield, taste, odor, and bulb color. Tuk Tuk and Trisula, the cultivars used in this experiment, have different bulb colors. Tuk Tuk’s bulb color is light red, while that of Trisula is dark red. This color difference may be attributed to variations in the metabolite contents of the shallot bulbs. The present experiment aimed to reveal differences in the metabolite contents of the two shallot cultivars by using Nuclear Magnetic Resonance (NMR) and then determine the specific metabolites contributing to these differences. Bulbs of Tuk Tuk and Trisula were planted in the field under the same conditions and then collected. The bulb samples were powdered, freeze-dried, and subjected to a two-phase extraction method with CDCl3 and D2O as solvents to separate the nonpolar metabolites from polar ones. The extracts were analyzed by 1H-NMR, and the spectra collected were analyzed using MNOVA software and Metaboanalyst.ca. A total of 23 metabolites were successfully identified and characterized in this experiment. The contents of eight of these metabolites, namely, sucrose, glutamine, citric acid, choline, methiin, propiin, threonine, and formic acid, were significantly higher in Trisula than in Tuk Tuk. These differences may be correlated with variations in the color intensity, pungency, and other traits of the cultivars. The results demonstrate that NMR metabolite profiling could effectively differentiate metabolite profile variations among shallot cultivars.

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