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The Sorghum bicolor genome and the diversification of grasses (2009)

A. H. Paterson ; J. E. Bowers ; R. Bruggmann ; [et al.]

Nature Publishing Group (NPG)

In: Nature. 457(7229): 551-6. doi: 10.1038/nature07723.

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Publication Date: 2009-02-04

Description: Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Paterson, Andrew H -- Bowers, John E -- Bruggmann, Remy -- Dubchak, Inna -- Grimwood, Jane -- Gundlach, Heidrun -- Haberer, Georg -- Hellsten, Uffe -- Mitros, Therese -- Poliakov, Alexander -- Schmutz, Jeremy -- Spannagl, Manuel -- Tang, Haibao -- Wang, Xiyin -- Wicker, Thomas -- Bharti, Arvind K -- Chapman, Jarrod -- Feltus, F Alex -- Gowik, Udo -- Grigoriev, Igor V -- Lyons, Eric -- Maher, Christopher A -- Martis, Mihaela -- Narechania, Apurva -- Otillar, Robert P -- Penning, Bryan W -- Salamov, Asaf A -- Wang, Yu -- Zhang, Lifang -- Carpita, Nicholas C -- Freeling, Michael -- Gingle, Alan R -- Hash, C Thomas -- Keller, Beat -- Klein, Patricia -- Kresovich, Stephen -- McCann, Maureen C -- Ming, Ray -- Peterson, Daniel G -- Mehboob-ur-Rahman -- Ware, Doreen -- Westhoff, Peter -- Mayer, Klaus F X -- Messing, Joachim -- Rokhsar, Daniel S -- England -- Nature. 2009 Jan 29;457(7229):551-6. doi: 10.1038/nature07723.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA. paterson@uga.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19189423" target="_blank"〉PubMed〈/a〉

Keywords: Arabidopsis/genetics ; Chromosomes, Plant/genetics ; *Evolution, Molecular ; Gene Duplication ; Genes, Plant ; Genome, Plant/*genetics ; Oryza/genetics ; Poaceae/*genetics ; Populus/genetics ; Recombination, Genetic/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Deletion/genetics ; Sorghum/*genetics ; Zea mays/genetics

Print ISSN: 0028-0836

Electronic ISSN: 1476-4687

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

Published by Nature Publishing Group (NPG)

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Genetic properties of the maize nested association mapping population (2009)

M. D. McMullen ; S. Kresovich ; H. S. Villeda ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 325(5941): 737-40. doi: 10.1126/science.1174320.

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Publication Date: 2009-08-08

Description: Maize genetic diversity has been used to understand the molecular basis of phenotypic variation and to improve agricultural efficiency and sustainability. We crossed 25 diverse inbred maize lines to the B73 reference line, capturing a total of 136,000 recombination events. Variation for recombination frequencies was observed among families, influenced by local (cis) genetic variation. We identified evidence for numerous minor single-locus effects but little two-locus linkage disequilibrium or segregation distortion, which indicated a limited role for genes with large effects and epistatic interactions on fitness. We observed excess residual heterozygosity in pericentromeric regions, which suggested that selection in inbred lines has been less efficient in these regions because of reduced recombination frequency. This implies that pericentromeric regions may contribute disproportionally to heterosis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McMullen, Michael D -- Kresovich, Stephen -- Villeda, Hector Sanchez -- Bradbury, Peter -- Li, Huihui -- Sun, Qi -- Flint-Garcia, Sherry -- Thornsberry, Jeffry -- Acharya, Charlotte -- Bottoms, Christopher -- Brown, Patrick -- Browne, Chris -- Eller, Magen -- Guill, Kate -- Harjes, Carlos -- Kroon, Dallas -- Lepak, Nick -- Mitchell, Sharon E -- Peterson, Brooke -- Pressoir, Gael -- Romero, Susan -- Oropeza Rosas, Marco -- Salvo, Stella -- Yates, Heather -- Hanson, Mark -- Jones, Elizabeth -- Smith, Stephen -- Glaubitz, Jeffrey C -- Goodman, Major -- Ware, Doreen -- Holland, James B -- Buckler, Edward S -- New York, N.Y. -- Science. 2009 Aug 7;325(5941):737-40. doi: 10.1126/science.1174320.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉United States Department of Agriculture-Agriculture Research Service (USDA-ARS), USA. mcmullenm@missouri.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19661427" target="_blank"〉PubMed〈/a〉

Keywords: Alleles ; Centromere/genetics ; *Chromosome Mapping ; Chromosomes, Plant/*genetics ; Crosses, Genetic ; Epistasis, Genetic ; Flowers/genetics/growth & development ; *Genetic Variation ; Genome, Plant ; Heterozygote ; Hybrid Vigor ; Inbreeding ; Linkage Disequilibrium ; Phenotype ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; *Quantitative Trait, Heritable ; Recombination, Genetic ; Selection, Genetic ; Zea mays/classification/*genetics/physiology

Print ISSN: 0036-8075

Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics

Published by American Association for the Advancement of Science (AAAS)

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The genetic architecture of maize flowering time (2009)

E. S. Buckler ; J. B. Holland ; P. J. Bradbury ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 325(5941): 714-8. doi: 10.1126/science.1174276.

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Publication Date: 2009-08-08

Description: Flowering time is a complex trait that controls adaptation of plants to their local environment in the outcrossing species Zea mays (maize). We dissected variation for flowering time with a set of 5000 recombinant inbred lines (maize Nested Association Mapping population, NAM). Nearly a million plants were assayed in eight environments but showed no evidence for any single large-effect quantitative trait loci (QTLs). Instead, we identified evidence for numerous small-effect QTLs shared among families; however, allelic effects differ across founder lines. We identified no individual QTLs at which allelic effects are determined by geographic origin or large effects for epistasis or environmental interactions. Thus, a simple additive model accurately predicts flowering time for maize, in contrast to the genetic architecture observed in the selfing plant species rice and Arabidopsis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Buckler, Edward S -- Holland, James B -- Bradbury, Peter J -- Acharya, Charlotte B -- Brown, Patrick J -- Browne, Chris -- Ersoz, Elhan -- Flint-Garcia, Sherry -- Garcia, Arturo -- Glaubitz, Jeffrey C -- Goodman, Major M -- Harjes, Carlos -- Guill, Kate -- Kroon, Dallas E -- Larsson, Sara -- Lepak, Nicholas K -- Li, Huihui -- Mitchell, Sharon E -- Pressoir, Gael -- Peiffer, Jason A -- Rosas, Marco Oropeza -- Rocheford, Torbert R -- Romay, M Cinta -- Romero, Susan -- Salvo, Stella -- Sanchez Villeda, Hector -- da Silva, H Sofia -- Sun, Qi -- Tian, Feng -- Upadyayula, Narasimham -- Ware, Doreen -- Yates, Heather -- Yu, Jianming -- Zhang, Zhiwu -- Kresovich, Stephen -- McMullen, Michael D -- New York, N.Y. -- Science. 2009 Aug 7;325(5941):714-8. doi: 10.1126/science.1174276.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉U.S. Department of Agriculture (USDA)-Agricultural Research Service (USDA-ARS), USA. esb33@cornell.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19661422" target="_blank"〉PubMed〈/a〉

Keywords: Alleles ; Chromosome Mapping ; Chromosomes, Plant/genetics ; Epistasis, Genetic ; Flowers/*genetics/growth & development ; Gene Frequency ; Genes, Plant ; Genetic Variation ; Geography ; Inbreeding ; Phenotype ; Polymorphism, Single Nucleotide ; *Quantitative Trait Loci ; Quantitative Trait, Heritable ; Recombination, Genetic ; Time Factors ; Zea mays/*genetics/growth & development/physiology

Print ISSN: 0036-8075

Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics

Published by American Association for the Advancement of Science (AAAS)

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Electronic Resource

Genetic diversity of Striga hermonthica and Striga asiatica populations in Kenya (2005)

GETHI, J G ; SMITH, M E ; MITCHELL, S E ; [et al.]

Oxford, UK : Blackwell Science Ltd

Weed research 45 (2005), S. 0

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ISSN: 1365-3180

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition

Notes: The parasitic angiosperms, Striga hermonthica and Striga asiatica, severely constrain cereal production in sub-Saharan Africa by causing huge losses in grain yield. Understanding the diversity of Striga populations is important because it allows identification of races or biotypes thus improving chances of breeding success. Amplified fragment length polymorphism (AFLP) analysis was used to study genetic diversity among 17 populations of S. asiatica and 24 populations of S. hermonthica from Kenya. A total of 349 DNA fragments ranging from 51 to 500 bp were obtained from four EcoRI and MseI primer combinations. Genetic distances for S. asiatica populations ranged from 0.009 to 0.116 with a mean of 0.032. S. hermonthica populations had a genetic distance that ranged from 0.007 to 0.025 with a mean of 0.015. Only two clusters were found in S. asiatica populations whereas no apparent structure was evident in S. hermonthica populations. There was no evidence of isolation by distance for the two species. Although the low genetic diversity suggests Striga is relatively uniform across the populations studied, it is possible that pathogenicity and virulence genes may be located in genomic regions that were not sampled. The data, however, does not provide evidence to support diversification of both Striga species in the region where the study was conducted.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1111/j.1365-3180.2004.00432.x

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