Prospects of breeding high-quality rice using post-genomic tools

Anacleto, Roslen; Cuevas, Rosa Paula; Jimenez, Rosario; Llorente, Cindy; Nissilä, Eero; Henry, Robert J.; Sreenivasulu, Nese

doi:10.1007/s00122-015-2537-6

Cited by 55 publications

(36 citation statements)

References 134 publications

(149 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Selected lines carrying targeted haplotypes from chromosomes 6 and 7 confirmed its influence on starch structure and grain digestibility. Grain quality genomics and systems genetics approaches were employed in this study to identify new haplotypes and regulatory networks responsible for starch structural variations in rice grain, which can be tapped to modulate grain digestibility in rice breeding pipelines using cutting-edge postgenomic marker-assisted technologies (Anacleto et al, 2015). This approach led to the discovery of rare allelic variations in the natural germplasm pool that code for more subtle alterations in grain digestibility, which can potentially be tapped to develop less digestible rice grains with superior grain quality to ensure consumer acceptance.…”

Section: Resultsmentioning

confidence: 99%

Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis

et al. 2016

Self Cite

View full text Add to dashboard Cite

A deeper understanding of the regulation of starch biosynthesis in rice (Oryza sativa) endosperm is crucial in tailoring digestibility without sacrificing grain quality. In this study, significant association peaks on chromosomes 6 and 7 were identified through a genomewide association study (GWAS) of debranched starch structure from grains of a 320 indica rice diversity panel using genotyping data from the high-density rice array. A systems genetics approach that interrelates starch structure data from GWAS to functional pathways from a gene regulatory network identified known genes with high correlation to the proportion of amylose and amylopectin. An SNP in the promoter region of Granule Bound Starch Synthase I was identified along with seven other SNPs to form haplotypes that discriminate samples into different phenotypic ranges of amylose. A GWAS peak on chromosome 7 between LOC_Os07g11020 and LOC_Os07g11520 indexed by a nonsynonymous SNP mutation on exon 5 of a bHLH transcription factor was found to elevate the proportion of amylose at the expense of reduced short-chain amylopectin. Linking starch structure with starch digestibility by determining the kinetics of cooked grain amylolysis of selected haplotypes revealed strong association of starch structure with estimated digestibility kinetics. Combining all results from grain quality genomics, systems genetics, and digestibility phenotyping, we propose target haplotypes for fine-tuning starch structure in rice through marker-assisted breeding that can be used to alter the digestibility of rice grain, thus offering rice consumers a new diet-based intervention to mitigate the impact of nutrition-related noncommunicable diseases.

show abstract

Section: Resultsmentioning

confidence: 99%

Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis

et al. 2016

Self Cite

View full text Add to dashboard Cite

show abstract

“…Wild rice populations are a key genetic resource for rice improvement (Anacleto et al ., 2015). The Australian populations may provide an especially useful resource for evaluation of rice domestication due to their isolation from significant impact of gene flow from domesticated rice.…”

Section: Discussionmentioning

confidence: 99%

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

Brożyńska

Copetti

Furtado

et al. 2017

Plant Biotechnology Journal

View full text Add to dashboard Cite

SummaryThe related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon‐like population, referred to as Taxon A, and O. meridionalis‐like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short‐ and long‐read next‐generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.

show abstract

“…These approaches are being adopted in crops of importance in developing countries such as in maize and wheat [121], rice [124], pulses (legumes) [11], cassava [118,120], cowpea [125], lentil [126], soybean [127,128], and pigeon pea [129]. With respect to the best practice for GS, various models are being put forward [113].…”

Section: Molecular Breedingmentioning

confidence: 99%

Perspectives on the Application of Next-generation Sequencing to the Improvement of Africa’s Staple Food Crops

Gedil¹,

Ferguson²,

Girma³

et al. 2016

Next Generation Sequencing - Advances, Applications and Challenges

View full text Add to dashboard Cite

The persistent challenge of insufficient food, unbalanced nutrition, and deteriorating natural resources in the most vulnerable nations, characterized by fast population growth, calls for utilization of innovative technologies to curb constraints of crop production. Enhancing genetic gain by using a multipronged approach that combines conventional and genomic technologies for the development of stress-tolerant varieties with high yield and nutritional quality is necessary. The advent of nextgeneration sequencing (NGS) technologies holds the potential to dramatically impact the crop improvement process. NGS enables whole-genome sequencing (WGS) and re-sequencing, transcriptome sequencing, metagenomics, as well as high-throughput genotyping, which can be applied for genome selection (GS). It can also be applied to diversity analysis, genetic and epigenetic characterization of germplasm and pathogen detection, identification, and elimination. High-throughput phenotyping, integrated data management, and decision support tools form the necessary supporting environment for effective utilization of genome sequence information. It is important that these opportunities for mainstreaming innovative breeding strategies, enabled by cutting-edge "Omics" technologies, are seized in Africa; however, several constraints must be addressed before the benefit of NGS can be fully realized. African breeding programs must have access to high-throughput genotyping facilities, capacity in the application of genome selection and marker-assisted breeding must be built and supported by capacity in genomic analysis and bioinformatics. This chapter demonstrates how interventions with NGS-enabled innovative strategies can be applied to increase genetic gain with insights from the Consortium of International

show abstract

Prospects of breeding high-quality rice using post-genomic tools

Cited by 55 publications

References 134 publications

Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis

Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

Perspectives on the Application of Next-generation Sequencing to the Improvement of Africa’s Staple Food Crops

Contact Info

Product

Resources

About