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1. Characterization of apomictic [BC.sub.7] and [BC.sub.8] pearl millet: meiotic chromosome behavior and construction of an ASGR-carrier chromosome-specific library

Author

Singh, M., Conner, J.A., Zeng, Y.-J., Hanna, W.W., Johnson, V.E., and Ozias-Akins, P.

Subjects
Pearl millet -- Research, Pearl millet -- Genetic aspects, Plant genetics -- Research, Agricultural industry, Business
Abstract

Apospory in Pennisetum squamulatum Fresen is inherited as a single-locus dominant trait. Molecular analysis has identified the apospory-specific genomic region (ASGR), a large segment of one chromosome that is necessary and sufficient to confer apomixis. To transfer apospory from P. squamulatum to pearl millet [P. glaucum (L.) R. Br.], advanced backcrosses were generated. Here we report the characterization of apomictic [BC.sub.7] and [BC.sub.8] generations. A [BC.sub.7]-derived genotype has two P. squamulatum chromosomes, while [BC.sub.8]-derived apomictic lines inherited only the ASGR chromosome that confers apospory to pearl millet. Morphologically, no significant differences were observed between backcross generations for plant height, leaf length, leaf width, and first internode and inflorescence lengths. However, the [BC.sub.7] and [BC.sub.8] lines differed significantly with regard to pollen viability, flowering time, and seed set. Pollen viability increased to 81% in the [BC.sub.8] lines compared with 37% in [BC.sub.7]. The frequency of aposporous embryo sacs was lower in [BC.sub.8] (79%) lines compared to [BC.sub.7] (93%). Meiotic behavior of chromosomes during metaphase I and anaphase I showed that [BC.sub.8] typically had a single univalent, identified as the ASGR chromosome by FISH (fluorescence in situ hybridization) and GISH (genomic in situ hybridization). Utilizing its unique behavior during meiosis the ASGR chromosome was microdissected and a chromosome-specific library was constructed and sequenced. Analysis of sequences identified both novel and previously known ASGR-linked sequences. doi: 10.2135/cropsci2009.05.0263

Published
2010

2. Erratum: Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

Author

Varshney, R.K., Shi, C., Thudi, M., Mariac, C., Wallace, J., Qi, P., Zhang, H., Zhao, Y., Wang, X., Rathore, A., Srivastava, R.K., Chitikineni, A., Fan, G., Bajaj, P., Punnuri, S., Gupta, S.K., Wang, H., Jiang, Y., Couderc, M., Katta, M.A.V.S.K., Paudel, D.R., Mungra, K.D., Chen, W., Harris-Shultz, K.R., Garg, V., Desai, N., Doddamani, D., Kane, N.A., Conner, J.A., Ghatak, A., Chaturvedi, P., Subramaniam, S., Yadav, O.P., Berthouly-Salazar, C., Hamidou, F., Wang, J., Liang, X., Clotault, J., Upadhyaya, H.D., Cubry, P., Rhoné, B., Gueye, M.C., Sunkar, R., Dupuy, C., Sparvoli, F., Cheng, S., Mahala, R.S., Singh, B., Yadav, R.S., Lyons, E., Datta, S.K., Hash, C.T., Devos, K.M., Buckler, E.S., Bennetzen, J.L., Paterson, A.H., Ozias-Akins, P., Grando, S., Mohapatra, T., Weckwerth, W., Reif, J.C., Liu, X., Vigouroux, Y., Xu, X., Varshney, R.K., Shi, C., Thudi, M., Mariac, C., Wallace, J., Qi, P., Zhang, H., Zhao, Y., Wang, X., Rathore, A., Srivastava, R.K., Chitikineni, A., Fan, G., Bajaj, P., Punnuri, S., Gupta, S.K., Wang, H., Jiang, Y., Couderc, M., Katta, M.A.V.S.K., Paudel, D.R., Mungra, K.D., Chen, W., Harris-Shultz, K.R., Garg, V., Desai, N., Doddamani, D., Kane, N.A., Conner, J.A., Ghatak, A., Chaturvedi, P., Subramaniam, S., Yadav, O.P., Berthouly-Salazar, C., Hamidou, F., Wang, J., Liang, X., Clotault, J., Upadhyaya, H.D., Cubry, P., Rhoné, B., Gueye, M.C., Sunkar, R., Dupuy, C., Sparvoli, F., Cheng, S., Mahala, R.S., Singh, B., Yadav, R.S., Lyons, E., Datta, S.K., Hash, C.T., Devos, K.M., Buckler, E.S., Bennetzen, J.L., Paterson, A.H., Ozias-Akins, P., Grando, S., Mohapatra, T., Weckwerth, W., Reif, J.C., Liu, X., Vigouroux, Y., and Xu, X.

Abstract

In the version of this article initially published, in the HTML, the wrong Creative Commons Attribution license (cc-by-nc rather than cc-by) was inserted. The error has been corrected in the HTML version of the article

Published
2018

3. Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

Author

Varshney, R.K., Shi, C., Thudi, M., Mariac, C., Wallace, J., Qi, P., Zhang, H., Zhao, Y., Wang, X., Rathore, A., Srivastava, R.K., Chitikineni, A., Fan, G., Bajaj, P., Punnuri, S., Gupta, S.K., Wang, H., Jiang, Y., Couderc, M., Katta, M.A.V.S.K., Paudel, D.R., Mungra, K.D., Chen, W., Harris-Shultz, K.R., Garg, V., Desai, N., Doddamani, D., Kane, N.A., Conner, J.A., Ghatak, A., Chaturvedi, P., Subramaniam, S., Yadav, O.P., Berthouly-Salazar, C., Hamidou, F., Wang, J., Liang, X., Clotault, J., Upadhyaya, H.D., Cubry, P., Rhoné, B., Gueye, M.C., Sunkar, R., Dupuy, C., Sparvoli, F., Cheng, S., Mahala, R.S., Singh, B., Yadav, R.S., Lyons, E., Datta, S.K., Hash, C.T., Devos, K.M., Buckler, E., Bennetzen, J.L., Paterson, A.H., Ozias-Akins, P., Grando, S., Mohapatra, T., Weckwerth, W., Reif, J.C., Liu, X., Vigouroux, Y., Xu, X., Varshney, R.K., Shi, C., Thudi, M., Mariac, C., Wallace, J., Qi, P., Zhang, H., Zhao, Y., Wang, X., Rathore, A., Srivastava, R.K., Chitikineni, A., Fan, G., Bajaj, P., Punnuri, S., Gupta, S.K., Wang, H., Jiang, Y., Couderc, M., Katta, M.A.V.S.K., Paudel, D.R., Mungra, K.D., Chen, W., Harris-Shultz, K.R., Garg, V., Desai, N., Doddamani, D., Kane, N.A., Conner, J.A., Ghatak, A., Chaturvedi, P., Subramaniam, S., Yadav, O.P., Berthouly-Salazar, C., Hamidou, F., Wang, J., Liang, X., Clotault, J., Upadhyaya, H.D., Cubry, P., Rhoné, B., Gueye, M.C., Sunkar, R., Dupuy, C., Sparvoli, F., Cheng, S., Mahala, R.S., Singh, B., Yadav, R.S., Lyons, E., Datta, S.K., Hash, C.T., Devos, K.M., Buckler, E., Bennetzen, J.L., Paterson, A.H., Ozias-Akins, P., Grando, S., Mohapatra, T., Weckwerth, W., Reif, J.C., Liu, X., Vigouroux, Y., and Xu, X.

Abstract

Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.

Published
2017

4. Single nucleotide Polymorphism–based genetic diversity in the Reference Set of Peanut ( Arachis spp.) by developing and applying cost‐effective kompetitive allele specific polymerase chain reaction genotyping assays

Author

Khera, P., Upadhyaya, H.D., Pandey, M.K., Roorkiwal, M., Sriswathi, M., Janila, P., Guo, Y., McKain, M.R., Nagy, E.D., Knapp, S.J., Leebens‐Mack, J., Conner, J.A., Ozias‐Akins, P., Varshney, R.K., Khera, P., Upadhyaya, H.D., Pandey, M.K., Roorkiwal, M., Sriswathi, M., Janila, P., Guo, Y., McKain, M.R., Nagy, E.D., Knapp, S.J., Leebens‐Mack, J., Conner, J.A., Ozias‐Akins, P., and Varshney, R.K.

Abstract

Kompetitive allele-specific polymerase chain reaction (KASP) assays have emerged as cost-effective marker assays especially for molecular breeding applications. Therefore, a set of 96 informative single nucleotide polymorphisms (SNPs) was used to develop KASP assays in groundnut or peanut (Arachis spp.). Developed assays were designated as groundnut KASP assay markers (GKAMs) and screened on 94 genotypes (validation set) that included parental lines of 27 mapping populations, seven synthetic autotetraploid and amphidiploid lines, and 19 wild species accessions. As a result, 90 GKAMs could be validated and 73 GKAMs showed polymorphism in the validation set. Validated GKAMs were screened on 280 diverse genotypes of the reference set for estimating diversity features and elucidating genetic relationships. Cluster analysis of marker allelic data grouped accessions according to their genome type, subspecies, and botanical variety. The subspecies Arachis hypogaea L. subsp. fastigiata Waldron and A. hypogaea subsp. hypogaea formed distinct cluster; however, some overlaps were found indicating their frequent intercrossing during the course of evolution. The wild species, having diploid genomes, were grouped into a single cluster. The average polymorphism information content value for polymorphic GKAMs was 0.32 in the validation set and 0.31 in the reference set. These validated and highly informative GKAMs may be useful for genetics and breeding applications in Arachis species.

Published
2013

6. Viewpoints

Author

Tamayo, Jesus G., Conner, J.A., Garza, Marcial, De la Fuente, Pamela S., Bodemann, Leroy, Wenker, Judith, Elder, John, and Mott, Kyle

Subjects
General interest, News, opinion and commentary
Published
2004

7. Viewpoints

Author

Maddocks, R.A., Jr., Gosch, B., Ledbetter, Hal, Conner, J.A., Lamm, Robert, Vann, Robert, Schmitz, Roger L., Starr, L.A., Greenwood, Jim, Jordan, M.J., Clanton, Brent, Botsford, Lindsay, Krohn, Matt, and Green, Jimmy

Subjects
General interest, News, opinion and commentary
Published
2004

8. Viewpoints

Author

Caldwell, Harry, Conner, J.A., Manning, Richard, Adams, Lisa, Marinos, Lou, Canfield, Pat, Musgrove, John G., and Haftings, Joyce

Subjects
General interest, News, opinion and commentary
Published
2004

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