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      Genetic architecture of purple pigmentation and tagging of some loci to SSR markers in pearl millet, Pennisetum glaucum (L.) R. Br.

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          Abstract

          This report describes the construction of integrated genetic maps in pearl millet involving certain purple phenotype and simple sequence repeat (SSR) markers. These maps provide a direct means of implementing DNA marker-assisted selection and of facilitating “map-based cloning” for engineering novel traits. The purple pigmentation of leaf sheath, midrib and leaf margin was inherited together ‘ en bloc’ under the control of a single dominant locus (the ‘midrib complex’) and was inseparably associated with the locus governing the purple coloration of the internode. The purple panicle was caused by a single dominant locus. Each of the three characters (purple lamina, purple stigma and purple seed) was governed by two complementary loci. One of the two loci governing purple seed was associated with the SSR locus Xpsmp2090 in linkage group 1, with a linkage value of 22 cM, while the other locus was associated with the SSR locus Xpsmp2270 in linkage group 6, with a linkage value of 23 cM. The locus for purple pigmentation of the midrib complex was either responsible for pigmentation of the panicle in a pleiotropic manner or was linked to it very closely and associated with the SSR locus Xpsmp2086 in linkage group 4, with a suggestive linkage value of 21 cM. A dominant allele at this locus seems to be a prerequisite for the development of purple pigmentation in the lamina, stigma and seed. These findings suggest that the locus for pigmentation of the midrib complex might regulate the basic steps in anthocyanin pigment development by acting as a structural gene while other loci regulate the formation of color in specific plant parts.

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          Most cited references 49

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          Easy calculations of lod scores and genetic risks on small computers.

           J Lalouel,  M Lathrop (1984)
          A computer program that calculates lod scores and genetic risks for a wide variety of both qualitative and quantitative genetic traits is discussed. An illustration is given of the joint use of a genetic marker, affection status, and quantitative information in counseling situations regarding Duchenne muscular dystrophy.
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            LOD significance thresholds for QTL analysis in experimental populations of diploid species

             Van Ooijen JW (1999)
            Linkage analysis with molecular genetic markers is a very powerful tool in the biological research of quantitative traits. The lack of an easy way to know what areas of the genome can be designated as statistically significant for containing a gene affecting the quantitative trait of interest hampers the important prediction of the rate of false positives. In this paper four tables, obtained by large-scale simulations, are presented that can be used with a simple formula to get the false-positives rate for analyses of the standard types of experimental populations with diploid species with any size of genome. A new definition of the term 'suggestive linkage' is proposed that allows a more objective comparison of results across species.
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              Molecular analysis of the maize anthocyanin regulatory locus C1.

              The C1 gene of maize plays a regulatory role in the production of anthocyanin pigments in the aleurone layer of the endosperm. As an initial step toward understanding the molecular details of how C1 controls pigment biosynthesis, we cloned the C1 gene. This was accomplished by first cloning a mutable allele of C1, c1-m5, which contains the transposable element Spm. A combination of molecular and genetic analysis was used to identify the Spm at the C1 locus. Individual genomic DNAs from a population in which the c1-mutable phenotype was segregating with the recessive c1 phenotype were digested with methyl-sensitive restriction enzymes and probed with a small DNA fragment derived from a defective Spm. One Sal I restriction fragment complementary to the Spm probe was shown to be present in the DNA of individuals with the c1-m5 phenotype but absent from DNA of individuals with a recessive c1 phenotype. Subsequent cloning and restriction analysis of this fragment revealed sequences flanking the Spm that proved to be C1-specific. A DNA fragment derived from the flanking sequences was then used as a probe to clone the wild-type C1 gene and several additional alleles of C1, including one stable recessive, two mutations caused by Ds insertions, one mutation induced by insertion of a defective Spm, and two dominant mutations, C1-S and C1-I. RNA blot hybridization analysis of three C1 alleles indicates that C1 regulation of the Bz1 and A1 structural genes in the anthocyanin biosynthetic pathway is at the transcriptional level.
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                Author and article information

                Journal
                Genet Mol Biol
                Genet. Mol. Biol
                GMB
                Genetics and Molecular Biology
                Sociedade Brasileira de Genética (Ribeirão Preto, SP, Brazil )
                1415-4757
                1678-4685
                Jan-Mar 2012
                16 February 2012
                : 35
                : 1
                : 106-118
                Affiliations
                [1 ]Plant Cytogenetics and Biotechnology Laboratory, Botany Department, Andhra University, Visakhapatnam, India
                [2 ]Global Theme-Biotechnology, ICRISAT, Patancheru, India
                Author notes
                Send correspondence to M.V. Subba Rao. Botany Department, Andhra University, 530003 Visakhapatnam, India. E-mail: mnpati_srao@ 123456yahoo.com .

                Associate Editor: Everaldo Gonçalves de Barros

                Article
                gmb-35-1-106
                3313498
                22481882
                Copyright © 2012, Sociedade Brasileira de Genética. Printed in Brazil

                License information: This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Categories
                Research Article

                Molecular biology

                gene tagging, pigmentation genetics, pearl millet

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