A gain-of-function mutation of OsMAPK6 leads to long grain in rice

Grain size is one of the most important agronomic traits controlling grain yield. Development of novel germplasm with large grains would be beneficial for crop improvement. We report the genetic identification and functional analysis of the LONG GRAIN 6(LOG6) gene, which is identical to MITOGENACTIVATED PROTEIN KINASE 6(OsMAPK6), affecting grain length of rice. Map-based cloning revealed that the long-grain phenotype of log6-D results from a glutamine(E) to lysine(K) mutation in the conserved TEY motif of OsMAPK6. In near-isogenic lines(NILs), the log6-D allele increased grain length and grain yield of Guichao 2(GC2), Teqing(TQ), and 93–11. Sequence analysis revealed 10 OsMAPK6 haplotypes,with xian(indica) and geng(japonica) harboring different haplotypes. Our findings shed light on the function of MAPKs and offer a novel dominant allele for improving the grain yield of rice.

Characterization of a novel high-tillering dwarf 3 mutant in rice

Tiller number and culm length are important components of plant architecture and determinate grain production in rice.A line SIL046, derived from an introgression lines population developed by an accession of common wild rice（Oryza rufipogon Griff.） and a high-yielding indica cultivar Guichao 2（Oryza sativa L.）,exhibits a higher tiller number and shorter culm length phenotype than the recipient parent Guichao 2（GC2）.Genetic analysis showed that the high-tillering dwarf phenotype was controlled by a novel single recessive gene,referred to as the high-tillering dwarf 3（htd3）,which located within the genetic distance of 13.4 cM between SSR makers RM7003 and RM277 on chromosome 12.By means of fine-mapping strategy,we mapped HTD3 gene within the genetic distance of 2.5 cM and the physical distance of 3100 kb in the centromere of chromosome 12.Further identification of HTD3 gene would provide a new opportunity to uncover the molecular mechanism of the development of culm and tiller,two important components of yields in rice.

四倍体野生稻快速驯化:启动人类新农业文明

通过人工选择优良遗传变异,将野生植物驯化为栽培作物,以满足人类对食物的需求,是人类发展历史中的重要事件,推动了人类文明的持续发展。随着世界人口持续增加,耕地面积不断减少,灾害性天气频发,全球粮食安全问题日趋严峻。基于作物驯化的分子机理及重要农艺性状的遗传基础,结合高通量基因组测序和高效基因组编辑技术,从头驯化野生植物,创造新型作物,将是应对这一挑战的有效策略之一。近日,中国科学院遗传与发育生物学研究所李家洋团队联合国内外多家单位,通过组装异源四倍体高秆野生稻(Oryza alta)基因组,优化遗传转化体系,利用基因组编辑技术,使其落粒性、芒性、株型、籽粒大小及抽穗期等决定作物驯化成功与否的重要性状发生改变,成功实现了异源四倍体高秆野生稻的从头定向驯化。该突破性研究成果证明了通过从头驯化将异源四倍体野生稻培育成未来的主粮作物,是确保粮食安全的可行策略,同时也为从头驯化野生和半野生植物、创制新型作物提供了重要参考。

GS6, A Member of the GRAS Gene Family,Negatively Regulates Grain Size in Rice

Grain size is an important yield-related trait in rice. Intensive artificial selection for grain size during domestication is evidenced by the larger grains of most of today＇s cultivars compared with their wild relatives. However, the molecular genetic control of rice grain size is still not well characterized. Here, we report the identification and cloning of Grain Size 6 （GS6）, which plays an important role in reducing grain size in rice. A premature stop at the ＋348 position in the coding sequence （CDS） of GS6 increased grain width and weight significantly. Alignment of the CDS regions of GS6 in 90 rice materials revealed three GS6 alleles. Most japonica varieties （95%） harbor the Type I haplotype, and 62.9% of indica varieties harbor the Type II haplotype. Association analysis revealed that the Type I haplotype tends to increase the width and weight of grains more than either of the Type II or Type III haplotypes. Further investigation of genetic diversity and the evolutionary mechanisms of GS6 showed that the GS6 gene was strongly selected in japonica cultivars. In addition, a ＂ggc＂ repeat region identified in the region that encodes the GRAS domain of GS6 played an important historic role in the domestication of grain size in rice. Knowledge of the function of GS6 might aid efforts to elucidate the molecular mechanisms that control grain development and evolution in rice plants, and could facilitate the genetic improvement of rice yield.

Natural Variations at TIG1 Encoding a TCP Tran scription Factor Contribute to Plant Architecture Domestication in Rice

The modification of plant architecture is a crucial target in rice domestication and modern genetic improvement.Although several genes regulating rice plant architecture have been characterized,the molecular mechanisms underlying rice plant architecture domestication remain largely unclear.Here we show that the inclined tiller growth in wild rice is controlled by a single dominant gene,TILLER INCLINED GROWTH 1 (T/Gf),which is located on chromosome 8 and encodes a TCP transcriptional activator.TIG1 is primarily expressed in the adaxial side of the tiller base,promotes cell elongation,and enlarges the tiller angle in wild rice.Variations in the TIG1 promoter of indica cultivars {tig1 allele) resulted in decreased expression of TIG1 in the adaxial side of tiller base and reduced cell length and tiller angle,leading to the transition from inclined tiller growth in wild rice to erect tiller growth during rice domestication.TIG1 positively regulates the expression of EXP A3,EXPB5,and SAUR39 to promote cell elongation and increase the tiller angle.Selective sweep analysis revealed that the tig1 allele was selected in indica cultivars by human beings.The cloning and characterization of TIG1 supports a new scenario of plant architecture evolution in rice.

NARROW AND ROLLED LEAF 2 regulates leaf shape,male fertility, and seed size in rice

Grain yield in rice （Oryza sativa L.） is closely related to leaf and flower development. Coordinative regulation of leaf, pollen, and seed development in rice as a critical biological and agricultural question should be addressed. Here we identified two allelic rice mutants with narrow and semi- rolled leaves, named narrow and rolled leaf2-1 （nrl2-1） and nr12- 2. Map-based molecular cloning revealed that NRL2 encodes a novel protein with unknown biochemical function. The mutation of NRL2 caused pleiotropic effects, including a reduction in the number of longitudinal veins, defective abaxial sclerenchymatous cell differentiation, abnormal tape- tum degeneration and microspore development, and the formation of more slender seeds compared with the wild type （WT）. The NRL2 protein interacted with Rolling-leaf （RL14）, causing the leaves of the nrl2 mutants to have a higher cellulose content and lower Iignin content than the WT, which may have been related to sclerenchymatous cell differentia- tion and tapetum degeneration. Thus, this gene is an essential developmental regulator controlling fundamental cellular and developmental processes, serving as a potential breeding target for high-yielding rice cultivars.

LHD1,an Allele of DTH8/Ghd8,Controls Late Heading Date in Common Wild Rice (Oryza rufipogon)

Flowering at suitable time is very important for plants to adapt to complicated environments and produce their seeds successfully for reproduction. In rice （Oryza rufipogon Griff.） photoperiod regulation is one of the important factors for controlling heading date. Common wild rice, the ancestor of cultivated rice, exhibits a late heading date and a more sensitive photoperiodic response than cultivated rice. Here, through map-based cloning, we identified a major quantitative trait loci （QTL） LHD1 （Late Heading Date 1）, an allele of DTH8/Ghd8, which controls the late heading date of wild rice and encodes a putative HAP3/NF-YB/CBF-A subunit of the CCAAT-box-binding transcription factor. Sequence analysis revealed that several variants in the coding region of LHD1 were correlated with a late heading date, and a further complementary study successfully rescued the phenotype. These results suggest that a functional site for LHD1 could be among those variants present in the coding region. We also found that LHD1 could down-regulate the expression of several floral transition activators such as Ehdl, Hd3a and RFT1 under long-day conditions, but not under short-day conditions. This indicates that LHD1 may delay flowering by repressing the expression of Ehdl, Hd3a and RFT1 under long-day conditions.

Molecular Evolution of the TACl Gene from Rice(Oryza sativa L.)

Tiller angle is a key feature of the architecture of cultivated rice （Oryza sativa）, since it determines planting density and influences rice yield. Our previous work identified Tiller Angle Control 1 （TACI） as a major quantitative trait locus that controls rice filler angle. To further clarify the evolutionary characterization of the TAC1 gene, we compared a TACl-containing 3164-bp genomic region among 113 cultivated varieties and 48 accessions of wild rice, including 43 accessions of O. rufipogon and five accessions of O. nivara. Only one single nucleotide polymorphism （SNP）, a synonymous substitution, was detected in TAC1 coding regions of the cultivated rice varieties, whereas one synonymous and one nonsynonymous SNP were detected among the TAC1 coding regions of wild rice accessions. These data indicate that little natural mutation and modification in the TAC1 coding region occurred within the cultivated rice and its progenitor during evolution. Nucleotide diversities in the TAC1 gene regions of O. sativa and O. rufipogon of 0.00116 and 0.00112, respectively, further indicate that TAC1 has been highly conserved during the course of rice domestication. A functional nucleotide polymorphism （FNP） of TAC1 was only found in the japonica rice group. A neutrality test revealed strong selection, especially in the 3＇-flanking region of the TAC1 coding region containing the FNP in the japonica rice group. However, no selection occurred in the indica and wild-rice groups. A phylogenetic tree derived from TAC1 sequence analysis suggests that the indica and japonica subspecies arose indepen- dently during the domestication of wild rice.

Microarray-Assisted Fine-Mapping of Quantitative Trait Loci for Cold Tolerance in Rice

Many important agronomic traits, including cold stress resistance, are complex and controlled by quantitative trait loci （QTLs）. Isolation of these QTLs will greatly benefit the agricultural industry but it is a challenging task. This study explored an integrated strategy by combining microarray with QTL-mapping in order to identify cold-tolerant QTLs from a cold-tolerant variety ILl12 at early-seedling stage. All the early seedlings of IL112 survived normally for 9 d at 4-5℃, while Guichao2 （GC2）, an indica cultivar, died after 4 d under the same conditions. Using the F2-3 population derived from the progeny of GC2 and ILl12, we identified seven QTLs for cold tolerance. Furthermore, we performed Affymetrix rice whole-genome array hybridization and obtained the expression profiles of ILl12 and GC2 under both low-temperature and normal conditions. Four genes were selected as cold QTL-related candidates, based on microarray data mining and QTL-mapping. One candidate gene, LOC_Os07g22494, was shown to be highly associated with cold tolerance in a number of rice varieties and in the F2-3 population, and its overexpression transgenic rice plants displayed strong tolerance to low temperature at early-seedling stage. The results indicated that overexpression of this gene （LOC_Os07g22494） could increase cold tolerance in rice seedlings. Therefore, this study provides a promising strategy for identifying candidate genes in defined QTL regions.

Harnessing Knowledge from Maize and Rice Domestication for New Crop Breeding

Crop domestication has fundamentally altered the course of human history,causing a shift from huntergatherer to agricultural societies and stimulating the rise of modern civilization.A greater understanding of crop domestication would provide a theoretical basis for how we could improve current crops and develop new crops to deal with environmental challenges in a sustainable manner.Here,we provide a comprehensive summary of the similarities and differences in the domestication processes of maize and rice,two major staple food crops that feed the world.We propose that maize and rice might have evolved distinct genetic solutions toward domestication.Maize and rice domestication appears to be associated with distinct regulatory and evolutionary mechanisms.Rice domestication tended to select de novo,loss-of-function,coding variation,while maize domestication more frequently favored standing,gain-offunction,regulatory variation.At the gene network level,distinct genetic paths were used to acquire convergent phenotypes in maize and rice domestication,during which different central genes were utilized,orthologous genes played different evolutionary roles,and unique genes or regulatory modules were acquired for establishing new traits.Finally,we discuss how the knowledge gained from past domestication processes,together with emerging technologies,could be exploited to improve modern crop breeding and domesticate new crops to meet increasing human demands.

RLS3, a protein with AAA+ domain localized in chloroplast, sustains leaf longevity in rice

Leaf senescence plays an important role in crop developmental processes that dramatically affect crop yield and grain quality. The genetic regulation of leaf senescence is complex, involving many metabolic and signaling pathways. Here, we identified a rapid leaf senescence 3 （rls3） mutant that displayed accelerated leaf senescence, shorter plant height and panicle length, and lower seed set rate than the wild type. Map-based cloning revealed that RLS3 encodes a protein with AAA＋ domain, localizing it to chloroplasts. Sequence analysis found that the rls3 8ene had a single-nucleotide substitution （G--~A） at the splice site of the Ioth intron/11th exon, resulting in the cleavage of the first nucleotide in 11th exon and premature termination of P, LS3 protein translation. Using transmission electron microscope, the chloroplasts of the rls3 mutant were observed to degrade much faster than those of the wild type. The investigation of the leaf senescence process under dark incubation conditions further revealed that the rls3 mutant displayed rapid leaf senescence. Thus, the RLS3 gene plays key roles in sustaining the normal growth of rice, while loss of function in RLS3 leads to rapid leaf senescence. The identification of RLS3 will be helpful to elucidate the mechanisms involved in leaf senescence in rice.

Analysis of QTLs for yield-related traits in Yuanjiang common wild rice (Oryza rufipogon Griff.)

Using an accession of common wild rice （Oryza rufipogon Griff.） collected from Yuanjiang County, Yunnan Province, China, as the donor and an elite cultivar 93-11, widely used in two-line indica hybrid rice production in China, as the recurrent parent, an advanced backcross populations were developed. Through genotyping of 187 SSR markers and investigation of six yield-related traits of two gen- erations （BC4F2 and BC4F4）, a total of 26 QTLs were detected by employing single point analysis and interval mapping in both genera-tions. Of the 26 QTLs, the alleles of 10 （38.5%） QTLs originating from O. rufipogon had shown a beneficial effect for yield-related traits in the 93-11 genetic background. In addition, five QTLs controlling yield and its components were newly identified, indicating that there are potentially novel alleles in Yuanjiang common wild rice. Three regions underling significant QTLs for several yield-related traits were detected on chromosome 1, 7 and 12. The QTL clusters were founded and corresponding agronomic traits of those QTLs showed highly significant correlation, suggesting the pleiotropism or tight linkage. Fine-mapping and cloning of these yield-related QTLs from wild rice would be helpful to elucidating molecular mechanism of rice domestication and rice breeding in the future.

Polyamine oxidase 3 is involved in salt tolerance at the germination stage in rice

Soil salinity inhibits seed germination and reduces seedling survival rate,resulting in significant yield reductions in crops.Here,we report the identification of a polyamine oxidase,OsPAO3,conferring salt tolerance at the germination stage in rice(Oryza sativa L.),through map-based cloning approach.OsPAO3 is up-regulated under salt stress at the germination stage and highly expressed in various organs.Overexpression of OsPAO3 increases activity of polyamine oxidases,enhancing the polyamine content in seed coleoptiles.Increased polyamine may lead to the enhance of the activity of ROS-scavenging enzymes to eliminate over-accumulated H;O;and to reduce Na;content in seed coleoptiles to maintain ion homeostasis and weaken Na;damage.These changes resulted in stronger salt tolerance at the germination stage in rice.Our findings not only provide a unique gene for breeding new salt-tolerant rice cultivars but also help to elucidate the mechanism of salt tolerance in rice.