Mapping and transcriptomic profiling reveal that the KNAT6 gene is involved in the dark green peel colour of mature pumpkin fruit (Cucurbita maxima L.)
{"title":"Mapping and transcriptomic profiling reveal that the KNAT6 gene is involved in the dark green peel colour of mature pumpkin fruit (Cucurbita maxima L.)","authors":"ChaoJie Wang, Wenqi Ding, Fangyuan Chen, Ke Zhang, Yuetong Hou, Guichao Wang, Wenlong Xu, Yunli Wang, Shuping Qu","doi":"10.1007/s00122-024-04741-7","DOIUrl":null,"url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Key message</h3><p>We identified a 580 bp deletion of <i>CmaKNAT6</i> coding region influences peel colour of mature <i>Cucurbita maxima</i> fruit.</p><h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>Peel colour is an important agronomic characteristic affecting commodity quality in <i>Cucurbit</i> plants. Genetic mapping of fruit peel colour promotes molecular breeding and provides an important basis for understanding the regulatory mechanism in <i>Cucurbit</i> plants. In the present study, the <i>Cucurbita maxima</i> inbred line ‘9-6’ which has a grey peel colour and ‘U3-3-44’ which has a dark green peel colour in the mature fruit stage, were used as plant materials. At 5–40 days after pollination (DAP), the contents of chlorophyll a, chlorophyll b, total chlorophyll and carotenoids in the ‘U3-3-44’ peels were significantly greater than those in the ‘9-6’ peels. In the epicarp of the ‘9-6’ mature fruit, the presence of nonpigmented cell layers and few chloroplasts in each cell in the pigmented layers were observed. Six generations derived by crossing ‘9-6’ and ‘U3-3-44’ were constructed, and the dark green peel was found to be controlled by a single dominant locus, which was named <i>CmaMg</i> (<i>mature green peel</i>). Through bulked-segregant analysis sequencing (BSA-seq) and insertion-deletion (InDel) markers, <i>CmaMg</i> was mapped to a region of approximately 449.51 kb on chromosome 11 using 177 F<sub>2</sub> individuals. Additionally, 1703 F<sub>2</sub> plants were used for fine mapping to compress the candidate interval to a region of 32.34 kb. Five coding genes were in this region, and <i>CmaCh11G000900</i> was identified as a promising candidate gene according to the reported function, sequence alignment, and expression analyses. <i>CmaCh11G000900</i> (<i>CmaKNAT6</i>) encodes the homeobox protein knotted-1-like 6 and contains 4 conserved domains. <i>CmaKNAT6</i> of ‘9-6’ had a 580 bp deletion, leading to premature transcriptional termination. The expression of <i>CmaKNAT6</i> tended to increase sharply during the early fruit development stage but decrease gradually during the late period of fruit development. Allelic diversity analysis of pumpkin germplasm resources indicated that the 580 bp deletion in the of <i>CmaKNAT6</i> coding region was associated with peel colour. Subcellular localization analysis indicated that CmaKNAT6 is a nuclear protein. Transcriptomic analysis of the inbred lines ‘9-6’ and ‘U3-3-44’ indicated that genes involved in chlorophyll biosynthesis were more enriched in ‘U3-3-44’ than in ‘9-6’. Additionally, the expression of transcription factor genes that positively regulate chlorophyll synthesis and light signal transduction pathways was upregulated in ‘U3-3-44’. These results lay a foundation for further studies on the genetic mechanism underlying peel colour and for optimizing peel colour-based breeding strategies for <i>C. maxima</i>.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"22 1","pages":""},"PeriodicalIF":4.4000,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Theoretical and Applied Genetics","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.1007/s00122-024-04741-7","RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"AGRONOMY","Score":null,"Total":0}
引用次数: 0
Key message
We identified a 580 bp deletion of CmaKNAT6 coding region influences peel colour of mature Cucurbita maxima fruit.
Abstract
Peel colour is an important agronomic characteristic affecting commodity quality in Cucurbit plants. Genetic mapping of fruit peel colour promotes molecular breeding and provides an important basis for understanding the regulatory mechanism in Cucurbit plants. In the present study, the Cucurbita maxima inbred line ‘9-6’ which has a grey peel colour and ‘U3-3-44’ which has a dark green peel colour in the mature fruit stage, were used as plant materials. At 5–40 days after pollination (DAP), the contents of chlorophyll a, chlorophyll b, total chlorophyll and carotenoids in the ‘U3-3-44’ peels were significantly greater than those in the ‘9-6’ peels. In the epicarp of the ‘9-6’ mature fruit, the presence of nonpigmented cell layers and few chloroplasts in each cell in the pigmented layers were observed. Six generations derived by crossing ‘9-6’ and ‘U3-3-44’ were constructed, and the dark green peel was found to be controlled by a single dominant locus, which was named CmaMg (mature green peel). Through bulked-segregant analysis sequencing (BSA-seq) and insertion-deletion (InDel) markers, CmaMg was mapped to a region of approximately 449.51 kb on chromosome 11 using 177 F2 individuals. Additionally, 1703 F2 plants were used for fine mapping to compress the candidate interval to a region of 32.34 kb. Five coding genes were in this region, and CmaCh11G000900 was identified as a promising candidate gene according to the reported function, sequence alignment, and expression analyses. CmaCh11G000900 (CmaKNAT6) encodes the homeobox protein knotted-1-like 6 and contains 4 conserved domains. CmaKNAT6 of ‘9-6’ had a 580 bp deletion, leading to premature transcriptional termination. The expression of CmaKNAT6 tended to increase sharply during the early fruit development stage but decrease gradually during the late period of fruit development. Allelic diversity analysis of pumpkin germplasm resources indicated that the 580 bp deletion in the of CmaKNAT6 coding region was associated with peel colour. Subcellular localization analysis indicated that CmaKNAT6 is a nuclear protein. Transcriptomic analysis of the inbred lines ‘9-6’ and ‘U3-3-44’ indicated that genes involved in chlorophyll biosynthesis were more enriched in ‘U3-3-44’ than in ‘9-6’. Additionally, the expression of transcription factor genes that positively regulate chlorophyll synthesis and light signal transduction pathways was upregulated in ‘U3-3-44’. These results lay a foundation for further studies on the genetic mechanism underlying peel colour and for optimizing peel colour-based breeding strategies for C. maxima.
期刊介绍：
Theoretical and Applied Genetics publishes original research and review articles in all key areas of modern plant genetics, plant genomics and plant biotechnology. All work needs to have a clear genetic component and significant impact on plant breeding. Theoretical considerations are only accepted in combination with new experimental data and/or if they indicate a relevant application in plant genetics or breeding. Emphasizing the practical, the journal focuses on research into leading crop plants and articles presenting innovative approaches.
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