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May 3, 2016

Gene duplication confers enhanced expression of 27-kDa ?-zein for endosperm modification in quality protein maize.

The maizeopaque2(o2) mutant has a high nutritional value but it develops a chalky endosperm that limits its practical use. Genetic selection foro2modifiers can convert the normally chalky endosperm of the mutant into a hard, vitreous phenotype, yielding what is known as quality protein maize (QPM). Previous studies have shown that enhanced expression of 27-kDa ?-zein in QPM is essential for endosperm modification. Taking advantage of genome-wide association study analysis of a natural population, linkage mapping analysis of a recombinant inbred line population, and map-based cloning, we identified a quantitative trait locus (q?27) affecting expression of 27-kDa ?-zein.q?27was mapped to the…

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May 3, 2016

The kiwifruit genome

The whole-genome sequence of Actinidia chinensis var. chinensis ‘Hongyang’ was published in 2013 and was represented as the first publicly available Ericales genome sequence. Publication in 2015 of an improved linkage map for A. chinensis and interspecific comparison analyses coupled with the availability of a second whole-genome sequence of a genotype closely related to ‘Hongyang’ have enabled the kiwifruit research community to improve the existing whole-genome sequence. This chapter describes the original genome sequence and steps towards its improvement.

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January 1, 2016

Effects of genome structure variation, homeologous genes and repetitive DNA on polyploid crop research in the age of genomics.

Compared to diploid species, allopolyploid crop species possess more complex genomes, higher productivity, and greater adaptability to changing environments. Next generation sequencing techniques have produced high-density genetic maps, whole genome sequences, transcriptomes and epigenomes for important polyploid crops. However, several problems interfere with the full application of next generation sequencing techniques to these crops. Firstly, different types of genomic variation affect sequence assembly and QTL mapping. Secondly, duplicated or homoeologous genes can diverge in function and then lead to emergence of many minor QTL, which increases difficulties in fine mapping, cloning and marker assisted selection. Thirdly, repetitive DNA sequences arising…

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October 8, 2015

Single molecule sequencing of THCA synthase reveals copy number variation in modern drug-type Cannabis sativa L.

Cannabinoid expression is an important genetically determined feature of cannabis that presents clinical and legal implications for patients seeking cannabinoid specific therapies like Cannabidiol (CBD). Cannabinoid, terpenoid, and flavonoid marker assisted selection can accelerate breeding efforts by offering genetic tools to select for desired traits at an early stage in growth. To this end, multiple models for chemotype inheritance have been described suggesting a complex picture for chemical phenotype determination. Here we explore the potential role of copy number variation of THCA Synthase using phased single molecule sequencing and demonstrate that copy number and sequence variation of this gene is…

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