SQUAMOSA Promoter Binding Protein-like Transcription Factors: Targets for Improving Cereal Grain Yield

Abstract

Grain size and shape are prime targets for crop breeders, as they affect both yield and quality of rice. In addition, breeders target plant vegetative and reproductive shoot architecture, because these traits influence grain number, and thus yield potential. Accordingly, genetic control of grain size and shape as well as shoot architecture has been extensively investigated in recent years. In a recent study, Bin Han and colleagues have used genome-wide association analysis of grain size in a diverse collection of rice varieties of worldwide origin and identified a major quantitative trait locus GLW7, which encodes a SQUAMOSA promoter binding protein-like 13 (OsSPL13), a member of the plant-specific SBP domain family of transcription factors (Si et al., 2016Si L. Chen J. Huang X. Gong H. Luo J. Hou Q. Zhou T. Lu T. Zhu J. Shangguan Y. et al.OsSPL13 controls grain size in cultivated rice.Nat. Genet. 2016; 48: 447-456Crossref PubMed Scopus (445) Google Scholar). GLW7 positively regulates the size of rice grain cells, thus increasing grain length. GLW7 also regulates rice reproductive shoot (panicle) architecture, and the combined effects of GLW7 on panicle and grain structure increase yield (Si et al., 2016Si L. Chen J. Huang X. Gong H. Luo J. Hou Q. Zhou T. Lu T. Zhu J. Shangguan Y. et al.OsSPL13 controls grain size in cultivated rice.Nat. Genet. 2016; 48: 447-456Crossref PubMed Scopus (445) Google Scholar). SPL proteins are relatively diverse in sequence and function, but all contain a highly conserved region of 76 amino acids known as the SBP domain. The first described SPL proteins were AmSBP1 and AmSBP2 from snapdragon (Antirrhinum majus), which bind to the promoter of floral meristem identity gene SQUAMOSA (Klein et al., 1996Klein J. Saedler H. Huijser P. A new family of DNA binding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA.Mol. Gen. Genet. 1996; 250: 7-16PubMed Google Scholar). Subsequently, SPL genes have been found to regulate diverse processes, including vegetative–reproductive phase change and shoot architecture. In Arabidopsis, SPL genes have been particularly implicated in regulating the timing of floral transition via both DELLA-dependent and DELLA-independent pathways (Wang et al., 2009Wang J.W. Czech B. Weigel D. miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana.Cell. 2009; 138: 738-749Abstract Full Text Full Text PDF PubMed Scopus (1000) Google Scholar, Yu et al., 2012Yu S. Galvão V.C. Zhang Y.C. Horrer D. Zhang T.Q. Hao Y.H. Feng Y.Q. Wang S. Schmid M. Wang J.W. Gibberellin regulates the Arabidopsis floral transition through miR156-targeted SQUAMOSA promoter binding-like transcription factors.Plant Cell. 2012; 24: 3320-3332Crossref PubMed Scopus (300) Google Scholar). Of particular interest is the fact that many SPL genes encode mRNAs with sequence complementarity with an evolutionarily conserved miR156. These mRNAs are specifically cleaved following interaction with miR156, and the miR156-SPL regulatory module functions as a master regulator for the age-dependent flowering responses (Wang et al., 2009Wang J.W. Czech B. Weigel D. miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana.Cell. 2009; 138: 738-749Abstract Full Text Full Text PDF PubMed Scopus (1000) Google Scholar). Although rice (Oryza sativa) genome contains 18 OsSPL genes (Preston and Hileman, 2013Preston J.C. Hileman L.C. Functional evolution in the plant SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) gene family.Front. Plant Sci. 2013; 4: 1-13Google Scholar), up to now none of these has been reported to modulate rice vegetative–reproductive phase changes, despite several of them appear to be concerned with the specification of plant vegetative or reproductive architecture, or of grain size or shape. For example, OsSPL14 plays important roles in controlling ideal plant architecture, and has major consequent effects on grain productivity (Jiao et al., 2010Jiao Y. Wang Y. Xue D. Wang J. Yan M. Liu G. Dong G. Zeng D. Lu Z. Zhu X. et al.Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice.Nat. Genet. 2010; 42: 541-544Crossref PubMed Scopus (944) Google Scholar, Miura et al., 2010Miura K. Ikeda M. Matsubara A. Song X.J. Ito M. Asano K. Matsuoka M. Kitano H. Ashikari M. OsSPL14 promotes panicle branching and higher grain productivity in rice.Nat. Genet. 2010; 42: 545-549Crossref PubMed Scopus (726) Google Scholar). Intriguingly, OsSPL14 plays opposing roles in the regulation of tiller and panicle branching. While upregulation of OsSPL14 expression leads to the production of fewer tillers with stronger, more robust culms, it conversely increases the number of panicle branches (Jiao et al., 2010Jiao Y. Wang Y. Xue D. Wang J. Yan M. Liu G. Dong G. Zeng D. Lu Z. Zhu X. et al.Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice.Nat. Genet. 2010; 42: 541-544Crossref PubMed Scopus (944) Google Scholar, Miura et al., 2010Miura K. Ikeda M. Matsubara A. Song X.J. Ito M. Asano K. Matsuoka M. Kitano H. Ashikari M. OsSPL14 promotes panicle branching and higher grain productivity in rice.Nat. Genet. 2010; 42: 545-549Crossref PubMed Scopus (726) Google Scholar). Similarly, transgenic plants with elevated levels of OsSPL13 expression have increased numbers of both primary and secondary panicle branches, whereas the numbers of panicle branches and grains per panicle are greatly reduced in RNAi lines with reduced levels of OsSPL13 expression (Si et al., 2016Si L. Chen J. Huang X. Gong H. Luo J. Hou Q. Zhou T. Lu T. Zhu J. Shangguan Y. et al.OsSPL13 controls grain size in cultivated rice.Nat. Genet. 2016; 48: 447-456Crossref PubMed Scopus (445) Google Scholar). Other SPLs are also known to be involved in the regulation of inflorescence architecture in contrasting ways: upregulation of OsSPL17 and OsSPL7 both reduce tiller numbers, while the downregulation of OsSPL17 or miR156-targeted OsSPL gene expression greatly reduces panicle branch numbers (Xie et al., 2006Xie K. Wu C. Xiong L. Genomic organization, differential expression, and interaction of SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice.Plant Physiol. 2006; 142: 280-293Crossref PubMed Scopus (480) Google Scholar, Wang et al., 2015aWang L. Sun S. Jin J. Fu D. Yang X. Weng X. Xu C. Li X. Xiao J. Zhang Q. Coordinated regulation of vegetative and reproductive branching in rice.Proc. Natl. Acad. Sci. USA. 2015; 112: 15504-15509Crossref Scopus (169) Google Scholar), except that overexpression of OsSPL16 reduces the numbers of both tillers and panicle branches (Wang et al., 2012Wang S. Wu K. Yuan Q. Liu X. Liu Z. Lin X. Zeng R. Zhu H. Dong G. Qian Q. Control of grain size, shape and quality by OsSPL16 in rice.Nat. Genet. 2012; 44: 950-954Crossref PubMed Scopus (794) Google Scholar). Taken together, these observations suggest that multiple OsSPL genes play redundant functions in regulating the activities of vegetative (tiller-forming) and inflorescence (panicle branch-forming) meristems, and often in contrasting ways (Figure 1). Recently, Si et al. (2016) reported that, in addition to regulating panicle architecture, OsSPL13 also promotes increases in the length and thickness of rice grain, but does not regulate grain width (Figure 1). Analysis at the cellular level (cell number and cell size) of the spikelet hull revealed that OsSPL13 regulates grain shape via control of the mechanisms determining cell size, and predominantly regulates organ development by regulating the size that individual cells achieve during growth, rather than the number of cells comprising an organ (Si et al., 2016Si L. Chen J. Huang X. Gong H. Luo J. Hou Q. Zhou T. Lu T. Zhu J. Shangguan Y. et al.OsSPL13 controls grain size in cultivated rice.Nat. Genet. 2016; 48: 447-456Crossref PubMed Scopus (445) Google Scholar). They also show that OsSPL13 binds to the promoter of a gene called SMALL AND ROUND SEED 5 (SRS5), and likely acts as a positive regulator of SRS5 expression. SRS5 encodes an α-tubulin subunit component of the microtubule cell growth machinery, thus providing a link between OsSPL13 and cell growth regulation. In contrast, another rice SPL-encoding gene, OsSPL16, the gene underlying the Grain-width 8 (GW8) QTL, is a positive regulator of cell proliferation and grain filling (Wang et al., 2012Wang S. Wu K. Yuan Q. Liu X. Liu Z. Lin X. Zeng R. Zhu H. Dong G. Qian Q. Control of grain size, shape and quality by OsSPL16 in rice.Nat. Genet. 2012; 44: 950-954Crossref PubMed Scopus (794) Google Scholar). High-level expression of OsSPL16 results in enhanced grain width and yield: cell division is promoted, cell numbers are increased, and thus grains become wider (Figure 1). OsSPL16 binds to the promoter of gene Os07g0603300 (the gene underlying another major rice grain shape QTL, GW7), and represses its expression (Wang et al., 2015bWang S. Li S. Liu Q. Wu K. Zhang J. Wang S. Wang Y. Chen X. Zhang Y. Gao C. et al.The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality.Nat. Genet. 2015; 47: 949-954Crossref Scopus (411) Google Scholar). Os07g0603300 encodes a TON1 RECRUIT MOTIF (TRM)-containing protein that likely recruits the TON1 protein to cortical microtubule arrays, thus influencing cell division patterns (Wang et al., 2015bWang S. Li S. Liu Q. Wu K. Zhang J. Wang S. Wang Y. Chen X. Zhang Y. Gao C. et al.The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality.Nat. Genet. 2015; 47: 949-954Crossref Scopus (411) Google Scholar, Wang et al., 2015cWang Y. Xiong G. Hu J. Jiang L. Yu H. Xu J. Fang Y. Zeng L. Xu E. Xu J. et al.Copy number variation at the GL7 locus contributes to grain size diversity in rice.Nat. Genet. 2015; 47: 944-948Crossref PubMed Scopus (391) Google Scholar). GW7 is a major quantitative trait locus for rice grain quality because it confers the much prized slender grain phenotype. The formation of slender grain is thus thought to be caused by an Os07g0603300-dependent alteration in the properties of the microtubules of the pre-prophase band of dividing cells that favors longitudinal over transverse organ growth, an alteration that is itself inhibited by OsSPL16-mediated transcriptional repression of Os07g0603300 (Wang et al., 2015bWang S. Li S. Liu Q. Wu K. Zhang J. Wang S. Wang Y. Chen X. Zhang Y. Gao C. et al.The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality.Nat. Genet. 2015; 47: 949-954Crossref Scopus (411) Google Scholar). Thus, different OsSPL genes affect grain size and shape in different ways, either by regulating cell elongation (OsSPL13), or by regulating the frequency or orientation of cell division events during cell proliferation (OsSPL16). It has been suggested that the ancestral SPL function was to regulate vegetative and floral transitions, this function has subsequently been partitioned through differential sub-functionalization following both gene duplication and speciation, and that neo-functionalization (e.g., in glume architecture) and parallel recruitment (e.g., in branching) occurred more recently in angiosperm evolution (Preston and Hileman, 2013Preston J.C. Hileman L.C. Functional evolution in the plant SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) gene family.Front. Plant Sci. 2013; 4: 1-13Google Scholar). While the liguleless gene (OsLG1) provides an important example of how the capturing of variation in SPL function was crucial to the origin of a closed panicle trait during rice domestication (Ishii et al., 2013Ishii T. Numaguchi K. Miura K. Yoshida K. Thanh P.T. Htun T.M. Yamasaki M. Komeda N. Matsumoto T. Terauchi R. et al.OsLG1 regulates a closed panicle trait in domesticated rice.Nat. Genet. 2013; 45: 462-465Crossref PubMed Scopus (130) Google Scholar), various rice examples discussed here provide powerful examples of how relatively rapid gene evolution, perhaps driven by post-domestication human selection, can contribute to the fine-tuning that has contributed to further improvements in crop performance. It is striking that so many of shoot branching and grain size/shape traits identified in rice QTL analyses are conferred by variant OsSPL genes, rather than by variance in genes belonging to other gene families. How was this rapid evolution of SPL function achieved? Changes in time, place or extent of SPL gene expression (e.g. 11 OsSPL genes were putative targets of miR156), alterations in downstream target gene specificity, and modulation of biochemical function of individual SPL proteins are all possible routes to functional variation. However, it is perhaps noteworthy that, in most of QTL examples discussed above, variation in the expression pattern of specific OsSPL genes confers trait variation, suggesting that this might be the major mechanism driving genetic variation selected during rice breeding programs. Irrespective of the mechanisms by which SPL functions evolved to regulate rice vegetative and reproductive shoot architecture and grain size/shape, it is clear that discovering and exploiting further useful genetic variation affecting SPL function is now a major goal for breeders seeking to improve grain yield, not only in rice but also in closely related cereal crops such as wheat, barley and maize.