Genomics‐assisted germplasm improvement

Rice is one of the most important staple cereals, feeding over 60% of China's population and contributes nearly 40% of the national total caloric intake (Cheng et al. 2007). A sustainable increase in rice production is required to meet the demands of increasing population and food consumption (Tilman et al. 2011). Over the past 50 years, rice yield has increased massively due to the development of semi-dwarf varieties and hybrid rice (Qian et al. 2016). However, rice production is stagnating and even falling in some regions, including China, threatened by the loss of arable farmland and urbanization associated with growing populations (Grassini et al. 2013). Therefore, it is urgent to develop new genetic resources and strategies to break the bottleneck and meet the increasing food demand (Guo et al. 2014; Rao et al. 2014). A focus on the high yield of rice will likely cause a serious sacrifice to superior quality rice, and this dilemma is especially apparent as the quality of some high-yield hybrid rice is generally poor. The superior quality rice is largely determined by high eating and cooking qualities, which is mainly judged by three primary physical and chemical characteristics of the starch in the endosperm: namely the amylose content, gel consistency, and gelatinization temperature (Fan et al. 2005). Zeng et al. (2017) have demonstrated that rational design is a powerful strategy for meeting the challenges of future crop breeding, particularly in pyramiding multiple complex traits. In this Special Issue, eight articles address germplasm improvement in rice and update the current status of rice production research in China. Two papers explore the regulation of grain yield in rice. Tang et al. (2018) report that transgenic rice plants overexpressing EcGDH from Eurotium cheralieri exhibit significantly enhanced aminating activities, providing a promising approach to improve nitrogen assimilation and, hence, increase grain yield in rice. Shen et al. (2018) performed CRISPR/Cas9-mediated quantitative trait loci (QTL) editing in five widely cultivated rice varieties and revealed that the same QTL can have diverse, even opposing, effects on grain yield in different genetic backgrounds. Four papers address various aspects of rice plant growth and development. Chloroplasts are specific organelles that are responsible for photosynthesis and other important metabolic pathways. Chloroplast genes are transcribed by the plastid-encoded RNA polymerase (PEP) or the nucleus-encoded RNA polymerase (NEP). He et al. (2018) report the characterization of a fructokinase-like protein 2 (HSA1/OsFLN2), a phosphofructokinase-B (PfkB)-type carbohydrate kinase that is a component of the PEP complex. Knockdown or knockout of the rice PfkB-type fructokinase OsFLN1, a close homolog of HSA1/OsFLN2, perturbs chloroplast biogenesis and causes a severe albino phenotype, along with seeding lethality. This study established that OsFLN1 and HSA1/OsFLN2 interact with THIOREDOXINZ (OsTRXz) to regulate chloroplast development. In the agronomic production of rice, trans-plantation shock represents an important problem. Shi et al. (2018) report the identification of a transplant-sensitive chloroplast-deficient (tsc1) rice mutant that exhibits albino leaves after transplantation. TSC1 encodes a noncanonical adenosine triphosphate (ATP) binding cassette (ABC) transporter, originating from cyanobacteria, which is indispensable for plastid development in the absence of light. Importantly, this study established that TSC1 mediates iron and copper balance to regulate prolamellar body formation, at the early P4 stage of leaf development, after transplantation. Huang et al. (2018) report the characterization of OsIDD2, a zinc finger and indeterminate domain (IDD) family transcription factor that is involved in the negative regulation of secondary cell wall formation, and other biological events, by downregulating its target genes. Gibberellins (GAs) are important phytohormones that modulate diverse plant developmental processes, including seed germination, leaf and stem elongation, floral transition, and reproductive development (Hedden and Sponsel 2015). Further insights into the role of GA functions, in rice, is provided by Li et al. (2018) who report that OsINO80, a conserved ATP-dependent chromatin-remodeling factor, acts in the regulation of the GA biosynthesis pathway to control many aspects of rice growth and development. Another article in this issue deals with biotic and abiotic stress tolerance. Rice diseases are a major challenge, and often result in significant crop loss. Thus, breeding for disease resistance has been a long-term goal of rice breeding programs. Zhang et al. (2018) report a rice spotted-leaf mutant, pelota displaying enhanced resistance to multiple races of Xanthomonas oryzae pv. oryzae. Map-based cloning revealed that OsPELOTA encodes a paralogue to eukaryotic release factor 1 (eRF1), which localizes to the endoplasmic reticulum and plasma membrane. Elevated levels of salicylic acid and decreased levels of jasmonate are detected in the pelota mutant. PELOTA protein is involved in bacterial leaf blight resistance by activating the salicylic acid metabolic pathway. Abiotic stresses such as drought, heat, cold and salinity adversely affect production and productivity of crops. Although calcium-dependent protein kinases (CPKs) are recognized as key messengers in plant stress, the specific roles of CPKs and the molecular mechanisms underlying their activity remain largely unknown. Liu et al. (2018) confirm that OsCPK24 is universally and highly expressed in rice plants and is induced by cold treatment. Knockdown of OsCPK24 resulted in increased sensitivity to cold, whereas OsCPK24 overexpression enhanced cold tolerance compared to the wide type. OsCPK24 phosphorylates OsGrx10, a glutathione-dependent thioltransferase, at rates modulated by changes in calcium concentration. Research in genomics-assisted germplasm improvement in rice has developed at a remarkable pace over recent years; for example, generation of “the giant rice”, “the sea rice”, “purple endosperm rice”, and so on. We anticipate that the articles in this Special Issue will contribute to furthering germplasm improvement in rice, and hence, to unlocking the potential for advancements in rice breeding. Special Issue Editor Qian Qian, Professor State Key Lab.