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The mutation of a PECTATE LYASE-LIKE gene is responsible for the Yellow Margin phenotype in potato

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Abstract

Key message

The yellow margin (ym) gene was mapped to a 30-kb genomic region in potato and the mutation of a pectate lyase gene led to this phenotype.

Abstract

The practice of clonally propagating potato (Solanum tuberosum L.), which has been lasted for thousands of years, has caused the accumulation of deleterious alleles. Despite yellow margin (ym) being a common cause of a detrimental weak-vigor phenotype and reduced yield in diploid potato, the underlying gene has eluded discovery to date. In this paper, we mapped the ym gene to a 30-kb region containing four annotated genes. Among them, PGSC0003DMG402023481 encodes a pectate lyase-like gene (StPLL) with lower expression in ym plants than in the wild-type plants. PCR amplification confirmed a 4.1-kb deletion in the mutant allele of StPLL. Knockout of StPLL in diploid potato resulted in a similar phenotype with the ym plants. This study not only characterizes the ym allele but also provides the molecular tools to select and purge it from populations, while also deepening our understanding of the morphogenesis in potato.

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Acknowledgements

We thank Henry De Jong for valuable suggestions to improve the manuscript. This research was funded by National Natural Science Foundation of China (No. 31601360), the Agricultural Science and Technology Innovation Program (ASTIP-CAAS), the Agricultural Science and Technology Innovation Program Cooperation and Innovation Mission (CAAS-XTCX2016), and Advanced Technology Talents in Yunnan Province (2013HA025).

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Authors and Affiliations

  1. College of Horticulture, Northwest Agriculture and Forest University, Yangling, 712100, Shaanxi, China

    Zhongmin Yang

  2. Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, Guangdong, China

    Zhongmin Yang, Die Tang, Sanwen Huang & Chunzhi Zhang

  3. College of Life Sciences, Nanjing Agricultural University, Nanjing, 210000, Jiangsu, China

    Shuangshuang Feng

  4. The AGIS-CAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650500, Yunnan, China

    Lidong Zhang & Yumei Li

  5. International Potato Center (CIP), CIP China Center Asia Pacific, Beijing, 100081, China

    Philip Kear

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  1. Zhongmin Yang
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  2. Shuangshuang Feng
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  3. Die Tang
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  6. Philip Kear
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  7. Sanwen Huang
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  8. Chunzhi Zhang
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Contributions

SH and CZ conceived and designed the experiments; ZY, SF, and LZ performed the experiments and analyzed the data; DT and YL performed the bioinformatics analyses; ZY performed the potato transformation; ZY, CZ, and PK wrote the paper; All authors have read and approved the final manuscript.

Corresponding authors

Correspondence to Sanwen Huang or Chunzhi Zhang.

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Conflict of interest

All authors declare that they have no conflict of interest.

Ethical standard

The experiments reported in this study comply with the current laws of China.

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Communicated by Albrecht E. Melchinger.

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Supplementary Fig. S1

Candidate interval sequence alignment and candidate allele amplification. a Alignment of resequencing data of normal and mutant plants using the IGV software. b PCR amplification of the StPLL in normal and mutant plants. Supplementary Fig. S2 Phylogenetic and conserved domain analysis of the StPLL protein. a Phylogenetic tree of StPLL and its homologs in Arabidopsis, the accession numbers are shown in the figure. b The PelC sequence in StPLL and its homologs in Arabidopsis. c Conserved domain analysis of StPLL and its alleles (PDF 3287 kb)

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Yang, Z., Feng, S., Tang, D. et al. The mutation of a PECTATE LYASE-LIKE gene is responsible for the Yellow Margin phenotype in potato. Theor Appl Genet 133, 1123–1131 (2020). https://doi.org/10.1007/s00122-020-03536-w

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  • DOI: https://doi.org/10.1007/s00122-020-03536-w

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