{"id":1067,"date":"2018-01-16T16:52:12","date_gmt":"2018-01-16T08:52:12","guid":{"rendered":"https:\/\/www.agrinoon.com\/agriculture\/?p=1067"},"modified":"2018-01-16T16:52:12","modified_gmt":"2018-01-16T08:52:12","slug":"maize-breeding-single-reference-not-enough","status":"publish","type":"post","link":"https:\/\/www.agrinoon.com\/agriculture\/2018\/01\/16\/maize-breeding-single-reference-not-enough\/","title":{"rendered":"Maize breeding: When a single reference is not enough"},"content":{"rendered":"

Keywords: maize<\/p>\n

Maize is amazingly diverse. A study <\/a>comparing genome segments from two inbred lines, for instance, revealed that half of the sequence and one-third of the gene content was not shared \u2013 that\u2019s more diversity within the species than between some other species, for example humans and chimpanzees, which exhibit more than 98 percent sequence similarity.<\/span><\/p>\n

So how can researchers and commercial breeders rely upon a single reference genome to represent the genetic diversity in their germplasms? More and more scientists are deciding they cannot.<\/span>
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At DuPont Pioneer, where DNA sequencing is paramount for R&D to reveal the genetic basis for traits of interest in a variety of commercial crops, an ambitious project has begun: A pan-genome reference collection based on high-speed, high throughput SMRT Sequencing and assembly.<\/span><\/p>\n

As described in this case study<\/a>, the company has developed a way to assemble high-quality reference genomes in one month. It has started to create them for several of their own elite breeding lines, as well as select wild strains.<\/span><\/p>\n

Having multiple genome assemblies of the same high standard for several genotypes will be increasingly important as researchers try to achieve a greater understanding of the impacts of structural variation on plant genomes, says Research Scientist Kevin Fengler, of the Data Science and Informatics group at DuPont Pioneer.<\/span><\/p>\n

\u201cWe want to focus on true structural variation. And we have confidence in the new discoveries we find in these genomes,\u201d he adds. \u201cUntil now, focusing on one reference genome has limited our view. We are just beginning to explore what we have been missing all along.\u201d<\/span><\/p>\n

Multiple Benefits<\/strong><\/span><\/h4>\n

From commercialization to crop improvement to answering basic questions about biology, generating and analyzing multiple reference genomes has myriad benefits in a variety of lab settings.<\/span><\/p>\n

\u201cIt has become clear that one single genome is not enough to represent the huge amount of variation in rice genomes,\u201d writes Zhi-Kang Li of the Chinese Academy of Agricultural Sciences in this recent Nature Scientific Data paper<\/a> about the assembly of an early-mature japonica rice genome.<\/span>
Rod Wing of the Arizona Genomics Institute agrees. He is aiming to build high-quality reference genomes for 23 additional species of rice using SMRT Sequencing. Beyond providing highly accurate, long-read sequence data, Wing said the PacBio platform is also useful for full-length RNA sequencing and its ability to characterize the methylome. As he notes in this blog post<\/a> and case study<\/a>, he can take rice tissues at several developmental stages and under many different environmental conditions, isolate RNA, and do Iso-Seq analysis on those samples to enable whole plant transcriptome analysis, which could help the community map gene networks.<\/span><\/p>\n

Other researchers are also eager to expand their set of references:<\/span><\/p>\n