Whole Genome Sequencing and Comparative Genomic Analysis Reveal Allelic Variations Unique to a Purple Colored Rice Landrace (Oryza sativa ssp. indica cv. Purpleputtu)
Purpleputtu (Oryza sativa ssp. indica cv. Purpleputtu) is a unique rice landrace from southern India that exhibits predominantly purple color. This study reports the underlying genetic complexity of the trait, associated domestication and de-domestication processes during its coevolution with presen...
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doaj-48e302fd6283486190c915d1c2d87b562020-11-25T00:55:11ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2019-05-011010.3389/fpls.2019.00513454137Whole Genome Sequencing and Comparative Genomic Analysis Reveal Allelic Variations Unique to a Purple Colored Rice Landrace (Oryza sativa ssp. indica cv. Purpleputtu)V. B. Reddy Lachagari0Ravi Gupta1Ravi Gupta2Sivarama Prasad Lekkala3Lakshmi Mahadevan4Lakshmi Mahadevan5Boney Kuriakose6Boney Kuriakose7Navajeet Chakravartty8A. V. S. K. Mohan Katta9Sam Santhosh10Arjula R. Reddy11George Thomas12George Thomas13AgriGenome Labs Pvt. Ltd., Biotechnology Incubation Center, MN iHub, Genome Valley, Hyderabad, IndiaMedgenome Labs Ltd., Bengaluru, IndiaSciGenom Labs Pvt. Ltd., Cochin, IndiaAgriGenome Labs Pvt. Ltd., Biotechnology Incubation Center, MN iHub, Genome Valley, Hyderabad, IndiaMedgenome Labs Ltd., Bengaluru, IndiaSciGenom Labs Pvt. Ltd., Cochin, IndiaSciGenom Research Foundation, Cheruthuruthy, IndiaAgriGenome Labs Pvt. Ltd., Kakkanad, IndiaAgriGenome Labs Pvt. Ltd., Biotechnology Incubation Center, MN iHub, Genome Valley, Hyderabad, IndiaAgriGenome Labs Pvt. Ltd., Biotechnology Incubation Center, MN iHub, Genome Valley, Hyderabad, IndiaSciGenom Research Foundation, Cheruthuruthy, IndiaDepartment of Plant Sciences, University of Hyderabad, Hyderabad, IndiaSciGenom Research Foundation, Cheruthuruthy, IndiaAgriGenome Labs Pvt. Ltd., Kakkanad, IndiaPurpleputtu (Oryza sativa ssp. indica cv. Purpleputtu) is a unique rice landrace from southern India that exhibits predominantly purple color. This study reports the underlying genetic complexity of the trait, associated domestication and de-domestication processes during its coevolution with present day cultivars. Along-with genome level allelic variations in the entire gene repertoire associated with the purple, red coloration of grain and other plant parts. Comparative genomic analysis using ‘a panel of 108 rice lines’ revealed a total of 3,200,951 variants including 67,774 unique variations in Purpleputtu (PP) genome. Multiple sequence alignment uncovered a 14 bp deletion in Rc (Red colored, a transcription factor of bHLH class) locus of PP, a key regulatory gene of anthocyanin biosynthetic pathway. Interestingly, this deletion in Rc gene is a characteristic feature of the present-day white pericarped rice cultivars. Phylogenetic analysis of Rc locus revealed a distinct clade showing proximity to the progenitor species Oryza rufipogon and O. nivara. In addition, PP genome exhibits a well conserved 4.5 Mbp region on chromosome 5 that harbors several loci associated with domestication of rice. Further, PP showed 1,387 unique when SNPs compared to 3,023 lines of rice (SNP-Seek database). The results indicate that PP genome is rich in allelic diversity and can serve as an excellent resource for rice breeding for a variety of agronomically important traits such as disease resistance, enhanced nutritional values, stress tolerance, and protection from harmful UV-B rays.https://www.frontiersin.org/article/10.3389/fpls.2019.00513/fullPurpleputturiceWGSSNPs/INDELsvariant callinganthocyanin pathway |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
V. B. Reddy Lachagari Ravi Gupta Ravi Gupta Sivarama Prasad Lekkala Lakshmi Mahadevan Lakshmi Mahadevan Boney Kuriakose Boney Kuriakose Navajeet Chakravartty A. V. S. K. Mohan Katta Sam Santhosh Arjula R. Reddy George Thomas George Thomas |
spellingShingle |
V. B. Reddy Lachagari Ravi Gupta Ravi Gupta Sivarama Prasad Lekkala Lakshmi Mahadevan Lakshmi Mahadevan Boney Kuriakose Boney Kuriakose Navajeet Chakravartty A. V. S. K. Mohan Katta Sam Santhosh Arjula R. Reddy George Thomas George Thomas Whole Genome Sequencing and Comparative Genomic Analysis Reveal Allelic Variations Unique to a Purple Colored Rice Landrace (Oryza sativa ssp. indica cv. Purpleputtu) Frontiers in Plant Science Purpleputtu rice WGS SNPs/INDELs variant calling anthocyanin pathway |
author_facet |
V. B. Reddy Lachagari Ravi Gupta Ravi Gupta Sivarama Prasad Lekkala Lakshmi Mahadevan Lakshmi Mahadevan Boney Kuriakose Boney Kuriakose Navajeet Chakravartty A. V. S. K. Mohan Katta Sam Santhosh Arjula R. Reddy George Thomas George Thomas |
author_sort |
V. B. Reddy Lachagari |
title |
Whole Genome Sequencing and Comparative Genomic Analysis Reveal Allelic Variations Unique to a Purple Colored Rice Landrace (Oryza sativa ssp. indica cv. Purpleputtu) |
title_short |
Whole Genome Sequencing and Comparative Genomic Analysis Reveal Allelic Variations Unique to a Purple Colored Rice Landrace (Oryza sativa ssp. indica cv. Purpleputtu) |
title_full |
Whole Genome Sequencing and Comparative Genomic Analysis Reveal Allelic Variations Unique to a Purple Colored Rice Landrace (Oryza sativa ssp. indica cv. Purpleputtu) |
title_fullStr |
Whole Genome Sequencing and Comparative Genomic Analysis Reveal Allelic Variations Unique to a Purple Colored Rice Landrace (Oryza sativa ssp. indica cv. Purpleputtu) |
title_full_unstemmed |
Whole Genome Sequencing and Comparative Genomic Analysis Reveal Allelic Variations Unique to a Purple Colored Rice Landrace (Oryza sativa ssp. indica cv. Purpleputtu) |
title_sort |
whole genome sequencing and comparative genomic analysis reveal allelic variations unique to a purple colored rice landrace (oryza sativa ssp. indica cv. purpleputtu) |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Plant Science |
issn |
1664-462X |
publishDate |
2019-05-01 |
description |
Purpleputtu (Oryza sativa ssp. indica cv. Purpleputtu) is a unique rice landrace from southern India that exhibits predominantly purple color. This study reports the underlying genetic complexity of the trait, associated domestication and de-domestication processes during its coevolution with present day cultivars. Along-with genome level allelic variations in the entire gene repertoire associated with the purple, red coloration of grain and other plant parts. Comparative genomic analysis using ‘a panel of 108 rice lines’ revealed a total of 3,200,951 variants including 67,774 unique variations in Purpleputtu (PP) genome. Multiple sequence alignment uncovered a 14 bp deletion in Rc (Red colored, a transcription factor of bHLH class) locus of PP, a key regulatory gene of anthocyanin biosynthetic pathway. Interestingly, this deletion in Rc gene is a characteristic feature of the present-day white pericarped rice cultivars. Phylogenetic analysis of Rc locus revealed a distinct clade showing proximity to the progenitor species Oryza rufipogon and O. nivara. In addition, PP genome exhibits a well conserved 4.5 Mbp region on chromosome 5 that harbors several loci associated with domestication of rice. Further, PP showed 1,387 unique when SNPs compared to 3,023 lines of rice (SNP-Seek database). The results indicate that PP genome is rich in allelic diversity and can serve as an excellent resource for rice breeding for a variety of agronomically important traits such as disease resistance, enhanced nutritional values, stress tolerance, and protection from harmful UV-B rays. |
topic |
Purpleputtu rice WGS SNPs/INDELs variant calling anthocyanin pathway |
url |
https://www.frontiersin.org/article/10.3389/fpls.2019.00513/full |
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