A Genome-Wide Analysis of the <i>Pentatricopeptide Repeat </i>(PPR) Gene Family and PPR-Derived Markers for Flesh Color in Watermelon (<i>Citrullus lanatus</i>)

A Genome-Wide Analysis of the <i>Pentatricopeptide Repeat </i>(PPR) Gene Family and PPR-Derived Markers for Flesh Color in Watermelon (<i>Citrullus lanatus</i>)

Watermelon (<i>Citrullus lanatus</i>) is an economically important fruit crop grown for consumption of its large edible fruit flesh. <i>Pentatricopeptide-repeat</i> (PPR) encoding genes, one of the large gene families in plants, are important RNA-binding proteins involved in...

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Main Authors: Saminathan Subburaj, Luhua Tu, Kayoun Lee, Gwang-Soo Park, Hyunbae Lee, Jong-Pil Chun, Yong-Pyo Lim, Min-Woo Park, Cecilia McGregor, Geung-Joo Lee
Format: Article
Language:English
Published: MDPI AG 2020-09-01
Series:Genes
Subjects:
watermelon
pentatricopeptide-repeat (PPR) gene family
comprehensive analysis
expression profiling
flesh color
Online Access:https://www.mdpi.com/2073-4425/11/10/1125
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spelling doaj-b3c7fcc8cfd945f2877c9fff6f651f652020-11-25T03:12:06ZengMDPI AGGenes2073-44252020-09-01111125112510.3390/genes11101125A Genome-Wide Analysis of the <i>Pentatricopeptide Repeat </i>(PPR) Gene Family and PPR-Derived Markers for Flesh Color in Watermelon (<i>Citrullus lanatus</i>)Saminathan Subburaj0Luhua Tu1Kayoun Lee2Gwang-Soo Park3Hyunbae Lee4Jong-Pil Chun5Yong-Pyo Lim6Min-Woo Park7Cecilia McGregor8Geung-Joo Lee9Department of Horticulture, Chungnam National University, Daejeon 34134, KoreaDepartment of Horticulture, Chungnam National University, Daejeon 34134, KoreaDepartment of Horticulture, Chungnam National University, Daejeon 34134, KoreaDepartment of Horticulture, Chungnam National University, Daejeon 34134, KoreaDepartment of Horticulture, Chungnam National University, Daejeon 34134, KoreaDepartment of Horticulture, Chungnam National University, Daejeon 34134, KoreaDepartment of Horticulture, Chungnam National University, Daejeon 34134, KoreaBreeding Institute, Hyundai Seed Co Ltd., Yeoju, Gyeonggi-do 12660, KoreaDepartment of Horticulture, University of Georgia, Athens, GA 30602, USADepartment of Horticulture, Chungnam National University, Daejeon 34134, KoreaWatermelon (<i>Citrullus lanatus</i>) is an economically important fruit crop grown for consumption of its large edible fruit flesh. <i>Pentatricopeptide-repeat</i> (PPR) encoding genes, one of the large gene families in plants, are important RNA-binding proteins involved in the regulation of plant growth and development by influencing the expression of organellar mRNA transcripts. However, systematic information regarding the PPR gene family in watermelon remains largely unknown. In this comprehensive study, we identified and characterized a total of 422 <i>C. lanatus </i>PPR (<i>ClaPPR</i>) genes in the watermelon genome. Most <i>ClaPPRs</i> were intronless and were mapped across 12 chromosomes. Phylogenetic analysis showed that <i>ClaPPR</i> proteins could be divided into P and PLS subfamilies. Gene duplication analysis suggested that 11 pairs of segmentally duplicated genes existed. In-silico expression pattern analysis demonstrated that <i>ClaPPRs </i>may participate in the regulation of fruit development and ripening processes. Genotyping of 70 lines using 4 single nucleotide polymorphisms (SNPs) from 4 <i>ClaPPRs</i> resulted in match rates of over 0.87 for each validated SNPs in correlation with the unique phenotypes of flesh color, and could be used in differentiating red, yellow, or orange watermelons in breeding programs. Our results provide significant insights for a comprehensive understanding of <i>PPR</i> genes and recommend further studies on their roles in watermelon fruit growth and ripening, which could be utilized for cultivar development of watermelon.https://www.mdpi.com/2073-4425/11/10/1125watermelonpentatricopeptide-repeat (PPR) gene familycomprehensive analysisexpression profilingflesh color
collection DOAJ
language English
format Article
sources DOAJ
author Saminathan Subburaj
Luhua Tu
Kayoun Lee
Gwang-Soo Park
Hyunbae Lee
Jong-Pil Chun
Yong-Pyo Lim
Min-Woo Park
Cecilia McGregor
Geung-Joo Lee
spellingShingle Saminathan Subburaj
Luhua Tu
Kayoun Lee
Gwang-Soo Park
Hyunbae Lee
Jong-Pil Chun
Yong-Pyo Lim
Min-Woo Park
Cecilia McGregor
Geung-Joo Lee
A Genome-Wide Analysis of the <i>Pentatricopeptide Repeat </i>(PPR) Gene Family and PPR-Derived Markers for Flesh Color in Watermelon (<i>Citrullus lanatus</i>)
Genes
watermelon
pentatricopeptide-repeat (PPR) gene family
comprehensive analysis
expression profiling
flesh color
author_facet Saminathan Subburaj
Luhua Tu
Kayoun Lee
Gwang-Soo Park
Hyunbae Lee
Jong-Pil Chun
Yong-Pyo Lim
Min-Woo Park
Cecilia McGregor
Geung-Joo Lee
author_sort Saminathan Subburaj
title A Genome-Wide Analysis of the <i>Pentatricopeptide Repeat </i>(PPR) Gene Family and PPR-Derived Markers for Flesh Color in Watermelon (<i>Citrullus lanatus</i>)
title_short A Genome-Wide Analysis of the <i>Pentatricopeptide Repeat </i>(PPR) Gene Family and PPR-Derived Markers for Flesh Color in Watermelon (<i>Citrullus lanatus</i>)
title_full A Genome-Wide Analysis of the <i>Pentatricopeptide Repeat </i>(PPR) Gene Family and PPR-Derived Markers for Flesh Color in Watermelon (<i>Citrullus lanatus</i>)
title_fullStr A Genome-Wide Analysis of the <i>Pentatricopeptide Repeat </i>(PPR) Gene Family and PPR-Derived Markers for Flesh Color in Watermelon (<i>Citrullus lanatus</i>)
title_full_unstemmed A Genome-Wide Analysis of the <i>Pentatricopeptide Repeat </i>(PPR) Gene Family and PPR-Derived Markers for Flesh Color in Watermelon (<i>Citrullus lanatus</i>)
title_sort genome-wide analysis of the <i>pentatricopeptide repeat </i>(ppr) gene family and ppr-derived markers for flesh color in watermelon (<i>citrullus lanatus</i>)
publisher MDPI AG
series Genes
issn 2073-4425
publishDate 2020-09-01
description Watermelon (<i>Citrullus lanatus</i>) is an economically important fruit crop grown for consumption of its large edible fruit flesh. <i>Pentatricopeptide-repeat</i> (PPR) encoding genes, one of the large gene families in plants, are important RNA-binding proteins involved in the regulation of plant growth and development by influencing the expression of organellar mRNA transcripts. However, systematic information regarding the PPR gene family in watermelon remains largely unknown. In this comprehensive study, we identified and characterized a total of 422 <i>C. lanatus </i>PPR (<i>ClaPPR</i>) genes in the watermelon genome. Most <i>ClaPPRs</i> were intronless and were mapped across 12 chromosomes. Phylogenetic analysis showed that <i>ClaPPR</i> proteins could be divided into P and PLS subfamilies. Gene duplication analysis suggested that 11 pairs of segmentally duplicated genes existed. In-silico expression pattern analysis demonstrated that <i>ClaPPRs </i>may participate in the regulation of fruit development and ripening processes. Genotyping of 70 lines using 4 single nucleotide polymorphisms (SNPs) from 4 <i>ClaPPRs</i> resulted in match rates of over 0.87 for each validated SNPs in correlation with the unique phenotypes of flesh color, and could be used in differentiating red, yellow, or orange watermelons in breeding programs. Our results provide significant insights for a comprehensive understanding of <i>PPR</i> genes and recommend further studies on their roles in watermelon fruit growth and ripening, which could be utilized for cultivar development of watermelon.
topic watermelon
pentatricopeptide-repeat (PPR) gene family
comprehensive analysis
expression profiling
flesh color
url https://www.mdpi.com/2073-4425/11/10/1125
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