Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement

Abstract Background The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies. Results Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus. Conclusions The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues.

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Genome assembly of the Chinese maize elite inbred line RP125 and its EMS mutant collection provide new resources for maize genetics research and crop improvement

The Plant Journal ◽

10.1111/tpj.15421 ◽

2021 ◽

Author(s):

Shujun Nie ◽

Bo Wang ◽

Haiping Ding ◽

Haijian Lin ◽

Li Zhang ◽

...

Keyword(s):

Inbred Line ◽

Genome Assembly ◽

Crop Improvement ◽

Genetics Research ◽

Maize Genetics ◽

Elite Inbred Line ◽

Mutant Collection

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Chromosome-level Genome Assembly of a Regenerable Maize Inbred Line A188

10.1101/2020.09.09.289611 ◽

2020 ◽

Author(s):

Guifang Lin ◽

Cheng He ◽

Jun Zheng ◽

Dal-Hoe Koo ◽

Ha Le ◽

...

Keyword(s):

Inbred Line ◽

Genome Assembly ◽

Single Copy ◽

Maize Inbred Line ◽

Genome Comparison ◽

Carotenoid Cleavage Dioxygenase ◽

Elevated Expression ◽

Enhanced Expression ◽

Low Expression ◽

Chromosome Level

ABSTRACTThe highly embryogenic and transformable maize inbred line A188 is an attractive model for analyzing maize gene function. Here we constructed a chromosome-level genome assembly of A188 using long reads and optical maps. Genome comparison of A188 with the reference line B73 identified pervasive structural variation, including a 1.8 Mb duplication on the Gametophyte factor1 locus for unilateral cross-incompatibility and six inversions of 0.7 Mb or greater. Increased copy number of the gene, carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression together with low expression of yellow endosperm 1 (y1) condition reduced carotenoid accumulation, which accounts for the white seed phenotype of A188 that contrasts with the yellow seed of B73 that has high expression of y1 and low expression of the single-copy ccd1. Further, transcriptome and epigenome analyses with the A188 reference genome revealed enhanced expression of defense pathways and altered DNA methylation patterns of embryonic callus.

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Effect of different proportions of exotic germplasm on grain yield and grain moisture in maize

Genetika ◽

10.2298/gensr1101067n ◽

2011 ◽

Vol 43 (1) ◽

pp. 67-73

Author(s):

Aleksandra Nastasic ◽

Mile Ivanovic ◽

Milisav Stojakovic ◽

Dusan Stanisavljevic ◽

Sanja Treskic ◽

...

Keyword(s):

Moisture Content ◽

Grain Yield ◽

Orthogonal Polynomials ◽

Inbred Line ◽

Male Parent ◽

Maize Inbred Line ◽

Exotic Germplasm ◽

Tropical Maize ◽

Maize Germplasm ◽

Grain Moisture

Two main questions in programs introgressing exotic maize germplasm into temperate materials are the choice of available exotic sources to work with, and the proportion of exotic germplasm that should be incorporated into adapted germplasm. The objective of this study was to compare effects of different proportions of tropical maize inbred line NC298 in hybrids male parent on grain yield and grain moisture content, using method of orthogonal polynomials. Methods of direct crosses and backcrosses were used to form four hybrid groups (six hybrids each) containing 0, 25, 50 and 75 percent of tropical exotic germplasm, respectively, by their male parent (or one half of mentioned proportions in the corresponding hybrids). The linear components of the germplasm proportions sum of squares, were significant (p<0.01) for both grain yield and moisture content and the cubic effect (p<0.05) for grain yield only. Results in this study clearly suggested backcross foundation populations with an adapted line to be appropriate selection sources for both grain yield and grain moisture content.

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Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics

The Crop Journal ◽

10.1016/j.cj.2021.08.002 ◽

2021 ◽

Author(s):

Fei Ge ◽

Jingtao Qu ◽

Peng Liu ◽

Lang Pan ◽

Chaoying Zou ◽

...

Keyword(s):

Functional Genomics ◽

Inbred Line ◽

Genome Assembly ◽

Reference Genome ◽

Maize Inbred Line

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SOMATIC EMBRYOGENESIS AND PLANT REGENERATION FROM AN ELITE TROPICAL MAIZE INBRED LINE

Revista Brasileira de Milho e Sorgo ◽

10.18512/rbms.v15i3.766 ◽

2017 ◽

Vol 15 (3) ◽

pp. 366

Author(s):

RAFAELI APARECIDA VIEIRA DE SOUZA ◽

MEIRE DE CÁSSIA ALVES ◽

NEWTON PORTILHO CARNEIRO ◽

ALUÍZIO BORÉM ◽

ANDRÉA ALMEIDA CARNEIRO

Keyword(s):

Inbred Line ◽

Embryogenic Callus ◽

Callus Formation ◽

Inbred Lines ◽

Maize Inbred Line ◽

Type Ii ◽

Tropical Maize ◽

Transformation Techniques ◽

N6 Medium

ABSTRACT – The improvement of tropical maize inbred lines by genetic transformation techniques remains a difficulttask since not all genotypes are capable of regenerating efficiently in vitro. The objective of this study was to evaluatethree different callus induction media, based on N6 or MS salts containing either 2,4-D (0, 2.5, 5.0, 10.0, 15.0, 30.0mg .L-1) or Dicamba (0; 0.25; 0.5; 1.0; 2.0; 4.0 mg.l-1) in the production of embryogenic callus from immature zygoticembryos of the tropical maize inbred line L3. Callus maturation was tested in MS medium containing 60 g.L-1 sucroseand supplemented with different combinations of BAP (0; 0.1; 0.5; 1.0 mg.L-1), NAA (0; 1.0 mg.L-1) and CuSO4 (0;1.25 mg.L-1). The L3 inbred line presented higher capacity for Type II callus formation on N6 medium content 10mg.L-1 2,4-D. For the maturation of callus, absence of plant growth regulators and addition of CuSO4 allowed higherpercentage of regeneration. The protocol developed presented 85% production of Type II embryogenic callus and 45%plant regeneration.Keywords: 2,4-D, dicamba, embryogenic callus, Zea mays.EMBRIOGÊNESE SOMÁTICA E REGENERAÇÃO DE PLANTAS A PARTIR DE UMA LINHAGEM DE MILHO TROPICAL ELITERESUMO – O melhoramento de linhagens de milho tropical através de técnicas de transformação genética continua aser uma tarefa difícil uma vez que nem todos os genótipos são capazes de regenerar eficientemente in vitro. O objetivodeste estudo foi avaliar três meios diferentes para a indução de calos embriogênicos, baseados em N6 ou MS saiscontendo 2,4-D (0; 2,5; 5,0; 10,0; 15,0; 30,0 mg.L-1) ou Dicamba (0; 0,25 ; 0,5; 1,0; 2,0; 4,0 mg.l-1) na produção decalos embriogênicos a partir de embriões zigóticos imaturos da linhagem de milho tropical elite L3. A maturação doscalos foi testada em meio MS com 60 g.L-1 de sacarose suplementado com diferentes combinações de BAP (0; 0,1; 0,5;1,0 mg.L-1), ANA (0; 1,0 mg.L-1) e CuSO4 (0; 1,25 mg L-1). A linhagem L3 apresentou alta capacidade para produçãode calos do Tipo II em meio N6 contendo 10 mg.L-1 de 2,4-D. Para a maturação dos calos, ausência de reguladoresde crescimento vegetal e adição de CuSO4 possibilitou maior porcentagem de regeneração. O protocolo desenvolvidoapresenta produção de 85% de calos embriogênicos do Tipo II e 45% de regeneração de plantas.Palavras-chave: 2,4-D, dicamba, calos embriogênicos, Zea mays.

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SOMATIC EMBRYOGENESIS AND PLANT REGENERATION FROM AN ELITE TROPICAL MAIZE INBRED LINE

Revista Brasileira de Milho e Sorgo ◽

10.18512/1980-6477/rbms.v15n3p366-376 ◽

2016 ◽

Vol 15 (3) ◽

pp. 366

Author(s):

RAFAELI APARECIDA VIEIRA DE SOUZA ◽

MEIRE DE CÁSSIA ALVES ◽

NEWTON PORTILHO CARNEIRO ◽

ALUÍZIO BORÉM ◽

ANDRÉA ALMEIDA CARNEIRO

Keyword(s):

Inbred Line ◽

Embryogenic Callus ◽

Callus Formation ◽

Maize Inbred Line ◽

Zygotic Embryos ◽

Type Ii ◽

Tropical Maize ◽

Transformation Techniques ◽

N6 Medium

ABSTRACT – The improvement of tropical maize inbred lines by genetic transformation techniques remains a difficult task since not all genotypes are capable of regenerating efficiently in vitro. The objective of this study was to evaluate three different callus induction media, based on N6 or MS salts containing either 2,4-D (0, 2.5, 5.0, 10.0, 15.0, 30.0 mg .L-1) or Dicamba (0; 0.25; 0.5; 1.0; 2.0; 4.0 mg.l-1) in the production of embryogenic callus from immature zygotic embryos of the tropical maize inbred line L3. Callus maturation was tested in MS medium containing 60 g.L-1 sucrose and supplemented with different combinations of BAP (0; 0.1; 0.5; 1.0 mg.L-1), NAA (0; 1.0 mg.L-1) and CuSO4 (0; 1.25 mg.L-1). The L3 inbred line presented higher capacity for Type II callus formation on N6 medium content 10 mg.L-1 2,4-D. For the maturation of callus, absence of plant growth regulators and addition of CuSO4 allowed higher percentage of regeneration. The protocol developed presented 85% production of Type II embryogenic callus and 45% plant regeneration.Keywords: 2,4-D, dicamba, embryogenic callus, Zea mays.EMBRIOGÊNESE SOMÁTICA E REGENERAÇÃO DE PLANTAS A PARTIR DE UMA LINHAGEM DE MILHO TROPICAL ELITERESUMO – O melhoramento de linhagens de milho tropical através de técnicas de transformação genética continua a ser uma tarefa difícil uma vez que nem todos os genótipos são capazes de regenerar eficientemente in vitro. O objetivo deste estudo foi avaliar três meios diferentes para a indução de calos embriogênicos, baseados em N6 ou MS sais contendo 2,4-D (0; 2,5; 5,0; 10,0; 15,0; 30,0 mg.L-1) ou Dicamba (0; 0,25 ; 0,5; 1,0; 2,0; 4,0 mg.l-1) na produção de calos embriogênicos a partir de embriões zigóticos imaturos da linhagem de milho tropical elite L3. A maturação dos calos foi testada em meio MS com 60 g.L-1 de sacarose suplementado com diferentes combinações de BAP (0; 0,1; 0,5; 1,0 mg.L-1), ANA (0; 1,0 mg.L-1) e CuSO4 (0; 1,25 mg L-1). A linhagem L3 apresentou alta capacidade para produção de calos do Tipo II em meio N6 contendo 10 mg.L-1 de 2,4-D. Para a maturação dos calos, ausência de reguladores de crescimento vegetal e adição de CuSO4 possibilitou maior porcentagem de regeneração. O protocolo desenvolvido apresenta produção de 85% de calos embriogênicos do Tipo II e 45% de regeneração de plantas.Palavras-chave: 2,4-D, dicamba, calos embriogênicos, Zea mays

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