Editing Cassava (section)

=== Genome ===

The complete and haplotype-resolved African cassava (TME204) genome has been reconstructed and made available using the Hi-C technology.<ref  name="Qi 2022">{{Cite journal |last1=Qi |first1=W. |last2=Lim |first2=Y. |last3=Patrignani |first3=A. |last4=Schläpfer |first4=P. |last5=Bratus-Neuenschwander |first5=A. |last6=Grüter |first6=S. |last7=Chanez |first7=C. |last8=Rodde |first8=N. |last9=Prat |first9=E. |last10=Vautrin |first10=S. |last11=Fustier |first11=M. |last12=Pratas |first12=D. |last13=Schlapbach |first13=R. |last14=Gruissem |first14=W. |display-authors=5 |year=2022 |title=The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features |journal=[[GigaScience]] |volume=11 |doi=10.1093/gigascience/giac028 |pmid=35333302 |pmc=8952263 }}</ref> The genome shows abundant novel gene loci with enriched functionality related to chromatin organization, meristem development, and cell responses.<ref  name="Qi 2022"/> Differentially expressed transcripts of different haplotype origins were enriched for different functionality during tissue development. In each tissue, 20–30% of transcripts showed allele-specific expression differences with <2% of direction-shifting. Despite high gene synteny, the HiFi genome assembly revealed extensive chromosome rearrangements and abundant intra-genomic and inter-genomic divergent sequences, with significant structural variations mostly related to long terminal repeat retrotransposons.<ref  name="Qi 2022"/>

Although [[smallholder]]s are otherwise [[economic efficiency|economically inefficient]] producers, they are vital to productivity at particular times.<ref name="McGregor 2020" /> Small cassava farmers are no exception.<ref name="McGregor 2020" /> [[Crop genetic diversity|Genetic diversity]] is vital when productivity has declined due to [[crop pest|pests]] and [[List of cassava diseases|diseases]], and smallholders tend to retain less productive but more diverse [[gene pool]]s.<ref name="McGregor 2020">{{cite journal |last1=McGregor  |first1=Andrew |last2=Manley |first2=M. |last3=Tubuna |first3=S. |last4=Deo |first4=R. |last5=Bourke |first5=Mike |date=2020 |journal=Pacific Economic Bulletin |publisher=Asia Pacific Press |title=Pacific Island food security: situation, challenges and opportunities |hdl=1885/39234}}</ref>

The molecular genetics of starchy root development in cassava have been analyzed and compared to other root and tuber crops, including possible (unproven) roles for
{{ visible anchor |Flowering Locus T |FT |FT protein |MeFT1 |MeFT2 }} (FT) orthologs.<ref name="Zierer 2021">{{cite journal |year=2021 |publisher=[[Annual Reviews (publisher)|Annual Reviews]] |issue=1 |volume=72 |pages=551–580 |first2=David |first4=Sophia |first1=Wolfgang |first3=Uwe |last4=Sonnewald |last3=Sonnewald |last2=Rüscher |last1=Zierer |journal=[[Annual Review of Plant Biology]] |doi=10.1146/annurev-arplant-080720-084456 |title=Tuber and Tuberous Root Development |pmid=33788583 |doi-access=free|bibcode=2021AnRPB..72..551Z }}</ref>