Copy number variation at the GL7 locus contributes to grain size diversity in rice.pdf

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Copy number variation at the GL7 locus contributes to grain size diversity in rice.pdf

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Copy number variation at the GL7 locus contributes to grain size diversity in rice

? 20 15 N at u re A m er ic a, In c. A ll ri g h ts r es er ve d . Nature GeNetics? ADVANCE ONLINE PUBLICATION l e t t e r s Copy?number?variants?(CNVs)?are?associated?with?changes? in?gene?expression?levels?and?contribute?to?various?adaptive? traits,2.?Here?we?show?that?a?CNV?at?the?Grain Length on Chromosome 7?(GL7)?locus?contributes?to?grain?size?diversity? in?rice?(Oryza sativa?L.).?GL7?encodes?a?protein?homologous? to?Arabidopsis thaliana?LONGIFOLIA?proteins,?which? regulate?longitudinal?cell?elongation.?Tandem?duplication? of?a?7.-kb?segment?at?the?GL7?locus?leads?to?upregulation? of?GL7?and?downregulation?of?its?nearby?negative?regulator,? resulting?in?an?increase?in?grain?length?and?improvement? of?grain?appearance?quality.?Sequence?analysis?indicates? that?allelic?variants?of?GL7?and?its?negative?regulator?are? associated?with?grain?size?diversity?and?that?the?CNV?at?the? GL7?locus?was?selected?for?and?used?in?breeding.?Our?work? suggests?that?pyramiding?beneficial?alleles?of?GL7?and?other? yield-?and?quality-related?genes?may?improve?the?breeding?of? elite?rice?varieties. Naturally occurring CNVs in individuals have the potential to drive phenotypic diversity in populations3. CNVs in plants tend to occur within the loci of stress-related genes4,5. Genome-wide studies have suggested that CNVs in rice are relatively recent events that arose within breeding populations6,7. However, whether and how CNVs are associated with specific traits still remains to be elucidated. Grain appearance is a major quality parameter that is determined by grain size and endosperm translucency8. The cloning and characteriza- tion of quantitative trait loci (QTLs), including GS3, GW2, GW5 (qSW5), GS5, GW8, GL3.1 (qGL3), TGW6 and Chalk5 (refs. 9–17), has enriched knowledge of how grain yield and quality are regulated and enables breeders to develop high-yield and good-quality varieties18. The landrace Ping13 (P13) is an indica variety with superior grain leng