Identification and characterization analysis of candidate genes controlling mushroom leaf development in Chinese kale by BSA-seq

Shuo Feng; Jianbing Wu; Kunhao Chen; Muxi Chen; Zhangsheng Zhu; Juntao Wang; Guoju Chen; Bihao Cao; Jianjun Lei; Changming Chen

doi:10.1007/s11032-023-01364-6

Identification and characterization analysis of candidate genes controlling mushroom leaf development in Chinese kale by BSA-seq

Mol Breed. 2023 Mar 3;43(3):17. doi: 10.1007/s11032-023-01364-6. eCollection 2023 Mar.

Authors

Shuo Feng^#¹, Jianbing Wu^#¹, Kunhao Chen^{2

3}, Muxi Chen^{2

3}, Zhangsheng Zhu¹, Juntao Wang¹, Guoju Chen¹, Bihao Cao¹, Jianjun Lei¹, Changming Chen¹

Affiliations

¹ Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China.
² Guangdong Helinong Agricultural Research Institute Co., Ltd, Shantou, 515800 Guangdong China.
³ Guangdong Helinong Biological Seed Industry Co., Ltd, Shantou, 515800 Guangdong China.

^# Contributed equally.

Abstract

Mushroom leaves (MLs) are malformed leaves that develop from the leaf veins in some of Chinese kale genotypes. To study the genetic model and molecular mechanism of ML development in Chinese kale, the F₂ segregation population was constructed by two inbred lines, genotype Boc52 with ML and genotype Boc55 with normal leaves (NL). In the present study, we have identified for the first time that the development of mushroom leaves may be affected by the change of adaxial-abaxial polarity of leaves. Examination of the phenotypes of F₁ and F₂ segregation populations suggested that ML development is controlled by two dominant major genes inherited independently. BSA-seq analysis showed that a major quantitative trait locus (QTL) qML4.1 that controls ML development is located within 7.4 Mb on chromosome kC4. The candidate region was further narrowed to 255 kb by linkage analysis combined with insertion/deletion (InDel) markers, and 37 genes were predicted in this region. According to the expression and annotation analysis, a B3 domain-containing transcription factor NGA1-like gene, BocNGA1, was identified as a key candidate gene for controlling ML development in Chinese kale. Fifteen single nucleotide polymorphisms (SNPs) were found in coding sequences and 21 SNPs and 3 InDels found in the promoter sequences of BocNGA1 from the genotype Boc52 with ML. The expression levels of BocNGA1 in ML genotypes are significantly lower than in the NL genotypes, which suggests that BocNGA1 may act as a negative regulator for ML genesis in Chinese kale. This study provides a new foundation for Chinese kale breeding and for the study of the molecular mechanism of plant leaf differentiation.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-023-01364-6.

Keywords: BSA-seq; BocNGA1 gene; Chinese kale; Gene mapping; Mushroom leaf.

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