Advances in Plant Breeding Strategies: Cereals by Jameel M. Al-Khayri & Shri Mohan Jain & Dennis V. Johnson

Author:Jameel M. Al-Khayri & Shri Mohan Jain & Dennis V. Johnson
Language: eng
Format: epub
ISBN: 9783030231088
Publisher: Springer International Publishing

7.8.8 Genome Sequencing

Yasui et al. (2016), using an inbred line of quinoa (Kd), reported an incomplete genome sequence. This novo genome assembly contained 25 K scaffolds consisting of 1 Gbp with N50 length of 86 kbp. The methodology used included sequencing on the Ilumina Hiseq 2500 and PacBio RS II sequencers.

A more complete sequence of the quinoa genome was made by Jarvis et al. (2017), using a coastal Chilean quinoa accession. It was observed an assembly of 439 sequence scaffolds that together covered 90% of the genome and aligned into 18 linkage groups. The total assembly size was 1.39 Gb. The methodology applied used single-molecule real time (SMRT) sequencing technology from Pacific Biosciences (PacBio), and optical chromosome-contact maps from BioNano Genomics and Dovetail Genomics, that include the SNP-based linkage map (Maughan et al. 2012) with two new linkage maps. Results of this research is a map with 6403 unique markers which span a total length of 2034 centimorgans (cM). This information suggests that quinoa genome could contains 44,776 genes.

A small genomic region encoding two transcription factors involved in saponin biosynthesis was also identified. Saponins confer a bitter taste to quinoa grains and are anti-nutritional compounds contained in the outer layer of the seeds. The amount of saponin present in the quinoa seeds depends on the genotype; some sweet accessions have been recognized. Jarvis et al. (2017) identified a mutation that causes alternative splicing, and a premature stop codon produces a truncated protein that results in reduced saponin production.

The identification of transmembrane proteins involved in salt tolerance were made by Schmockel et al. (2017), using quinoa genome sequence assembled by Jarvis et al. (2017), combined with RNA-seq analysis, comparative genomics and topology prediction. They identified 219 candidate genes, which were reduced to 15 genes by looking at single nucleotide polymorphisms. Additionally, large variation in salinity tolerance were observed among 21 Chenopodium accessions (14 C. quinoa, 5 C. berlandieri and 2 C. hircimum), with C. hircimum having the highest tolerance to salinity.

ABA-independent expression patterns were observed by Morales et al. (2017) studying the transcriptional responses of R49, the most drought tolerant genotype of three Chilean quinoas under drought conditions. The transcriptome of R49 was sequenced by the Illumina pair-ends method, using total RNA extracted from quinoa plants under drought stress and from total RNA extracted from control plants. Results showed that 1579 genes were over-represented under drought conditions, and 877 were underrepresented. Of the genes that were overrepresented, 19% were unknown genes, indicating that the drought response in quinoa might have several paths that are still unknown.

Liu et al. (2018) analyzed the Chenoposium quinoa genome and identified 16 Hsp70 members of heat-shock proteins with important roles in response to biotic and abiotic stress . Phylogenetic analysis revealed the independent origination of those Hsp70 members, with 8 paralogous pairs comprising the Hsp70 family in quinoa. Additionally gene expression analyses revealed significant variations of Cqhsp70s in response to drought stress.

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