Rice is a main food source for more than half of the global population and is a model plant for genome-based research.

Since the turn of the century, Chinese scientists have embarked on a "Long March" toward more intricate understanding of the complex agronomic traits of rice, spurred in part by the completion of the draft genome sequence of the indica variety 93-11 and a fine sequence analysis of chromosome 4 of the japonica variety Nipponbare.

These researchers "have made crucial contributions to international efforts in sequencing the rice genome," report Jianru Zuo and Jiayang Li, scientists at the State Key Laboratory of Plant Genomics and National Plant Gene Research Center, part of the Chinese Academy of Sciences, in Beijing.

"Researchers have made rapid and impressive progress on almost every aspect of rice biology by employing a genetics-based strategy," they add in a new study published in the Beijing-based journal National Science Review.

The scientists review key advances made in recent years in deepening understanding of the rice genome and outstanding agronomic traits.

These advances extend to the molecular mechanisms involved in rice shoot formation, root development and nutrition, leaf development, heading and panicle development, fertility, seed development, seed shattering, grain quality, resistance to biotic and abiotic stress, as well as to the structure, evolution and regulation of the rice genome.

Great progress has been made in rice developmental biology

In rice, the shoot architecture is mainly determined by the number of shoots (known as tillers or culms in rice) per plant, tiller angle and plant height. The identification and characterization of the MOC1, LAX2, TAD1, OsMADS57, D27, IPA1/WFP, LAZY1, LPA1, PROG1 and BC12/GDD1 genes have created a key foundation for understanding the molecular mechanisms in rice shoot architecture (Figure 1).

SLL1/RL9, OsCslD4, LIC1, DLT, XIAO, OsGSR1, ILA1, LC2 and NAL1 are critical genes in leaf architecture, including the size, shape and the angle related to the stem, to determine the photosynthetic efficiency and planting density; OsRAA1, OsORC3, OsPHR2, LTN1, OsPHF1 and OsMYB2B-1 are involved in the regulation of root development and nutrition.

Key genes in the regulation of flowering time (heading date in crops) and panicle development have been addressed in detail including RID1, Ghd7, DTH2, Ehd4, DTH8, EL1, ETR2, LC2, EG1, CFO1, OsMADS15, OsMADS1, DEP1, EP2 and Gn1a. Ghd7, SP1 and OsARG play an important role in panicle development.

In terms of reproductive developmental biology, CRC1, PAIR3, MER3, ZEP1, ZIP4, OsSGO1, HEI10 and OsCOM1 are involved in the regulation of meiosis; CSA and PSS1 participate in the regulation of male gametophyte development; DR, EAT1 and API5 are responsible for the development of tapetal cells; MTR1 plays a critical role in mediating the interaction between sporophytic and reproductive cells; and WA352, ORFH79, RF5 and ORF5 are major genes in regulating fertility.

Grain size and shape are important determinants of grain yield and quality in cereal crops. There are several genes, including GS3, GS5, GW2, GW5, GW8, qGL3/qGL3.1, PHD1, GIF1 and OsMADS29, involved in regulating this process. The seed shattering in wild rice is controlled by the SHA1 gene. Waxy, ALK, RSR1 and FGR are responsible for control of grain quality.

As far as biotic resistance and abiotic stress tolerance are concerned, OsMPK6, C3H12, XA13, GH3-8, NLS1, PIK-1, PIK-2, LYP4, LYP6, OsBBI1 and BPH14 are involved in rice-pathogen/insect interaction; SKC1, DST, OsSKIPa, DSM1, OsSIK1, DSM2, OsbZIP23, OsbZIP46, ABL1 and OsTRXh1 play a role in tolerance to abiotic factors such as salinity, cold and drought stresses.

By sequencing 517 rice landraces, more than 3.6 million SNPs were identified; subsequent genome-wide association study (GWAS) of 14 agronomic traits in the indica subspecies identified more than one third of the phenotypic variance; in another immense effort, a larger and more diverse sample of 950 worldwide rice varieties were analyzed and subjected to GWAS, resulting in the identification of 32 new loci associated with flowering time and 10 loci with grain-related traits.

During the past several years, Chinese scientists have identified and functionally characterized more than 140 agronomically important genes in rice, and made breakthrough discoveries in terms of mechanisms of molecular regulation.

"Many of the cloned genes encode novel proteins with unknown biochemical functions, thus preventing mechanistic understanding on the related traits," state the co-authors of the new study, who are based at the Institute of Genetics and Developmental Biology in Beijing. "It also should be noted that many agronomic traits, especially those involved in adaptability in response to environmental alterations, are subjected to epigenetic regulation, and the underlying mechanisms are, unfortunately, poorly understood."

"Importantly, as demonstrated by several recent studies, the analysis of the dynamic changes of the rice genome during evolution and domestication in combined with GWAS, powered by the next-generation sequencing and other technologies, should allow fast and efficient identification of important trait-associated loci and alleles that are difficult to be identified by the genetic approach," they add.

"With molecular marker-assisted selection and newly developed genome editing technology, these agronomically important traits should be molecularly designed and eventually pyramided in the new generations of super rice varieties."

Jianru Zuo and Jiayang Li. "Molecular dissection of complex agronomic traits of rice: a team effort by Chinese scientists in recent years." Natl Sci Rev (June 2014) 1 (2): 253-276