亚洲栽培稻主要驯化性状研究进展

水稻是研究谷类作物驯化的良好材料, 其中种子落粒性消失、休眠性减弱和株型上的变化是水稻驯化过程中的3个关键事件, 造就了高产、发芽整齐及可密植的现代水稻。落粒性丧失一直被认为是野生稻驯化形态学上的最直接证据, 而控制落粒的主要基因Sh4和qSH1分别暗示不同的水稻驯化历史。种子休眠性的减弱适应了现代农业生产上同步发芽的需求, Sdr4、qSD7-1和qSD12基因是目前已知的调控种子休眠性的3个关键位点。野生稻匍匐生长等特点与其长期所在的易变生境有关, 而栽培稻的直立生长形态则适应了农业上密植生产的需要, 受PROG1等基因控制。野生稻的异交特性促进了驯化基因在群体间传播, 而自花授粉则使驯化基因得以稳定遗传, 从而加快人工选择的累积。目前的水稻驯化研究侧重于单基因或一些中性标记, 而对控制驯化性状的网络化通路的进化研究却相对缺乏。随着功能基因组研究的深入, 驯化性状的分子机理将会被全面揭示, 而基于此的网络化通路研究必将更加真实地反应水稻驯化过程。文章综述了水稻关键驯化性状分子机理的研究进展, 为驯化基因网络的研究提供参考, 也为水稻分子设计改良提供新的思路。     

TAC1, a major quantitative trait locus controlling tiller angle in rice

A critical step during rice (Oryza sativa) cultivation is dense planting: a wider tiller angle will increase leaf shade and decrease photosynthesis efficiency, whereas a narrower tiller angle makes for more efficient plant architecture. The molecular basis of tiller angle remains unknown. This research demonstrates that tiller angle is controlled by a major quantitative trait locus, TAC1 (Tiller Angle Control 1). TAC1 was mapped to a 35-kb region on chromosome 9 using a large F(2) population from crosses between an indica rice, IR24, which displays a relatively spread-out plant architecture, and an introgressed line, IL55, derived from japonica rice Asominori, which displays a compact plant architecture with extremely erect tillers. Genetic complementation further identified the TAC1 gene, which harbors three introns in its coding region and a fourth 1.5-kb intron in the 3'-untranslated region. A mutation in the 3'-splicing site of this 1.5-kb intron from 'AGGA' to 'GGGA' decreases the level of tac1, resulting in a compact plant architecture with a tiller angle close to zero. Further sequence verification of the mutation in the 3'-splicing site of the 1.5-kb intron revealed that the tac1 mutation 'GGGA' was present in 88 compact japonica rice accessions and TAC1 with 'AGGA' was present in 21 wild rice accessions and 43 indica rice accessions, all with the spread-out form, indicating that tac1 had been extensively utilized in densely planted rice grown in high-latitude temperate areas and at high altitudes where japonica rice varieties are widely cultivated.     

TAC4 controls tiller angle by regulating the endogenous auxin content and distribution in rice

Tiller angle, an important component of plant architecture, greatly influences the grain yield of rice (Oryza sativa L.). Here, we identified Tiller Angle Control 4 (TAC4) as a novel regulator of rice tiller angle. TAC4 encodes a plant‐specific, highly conserved nuclear protein. The loss of TAC4 function leads to a significant increase in the tiller angle. TAC4 can regulate rice shoot gravitropism by increasing the indole acetic acid content and affecting the auxin distribution. A sequence analysis revealed that TAC4 has undergone a bottleneck and become fixed in indica cultivars during domestication and improvement. Our findings facilitate an increased understanding of the regulatory mechanisms of tiller angle and also provide a potential gene resource for the improvement of rice plant architecture.     

2012年第11期《遗传》封面说明

作物的驯化是人类从开始种植和储存的野生作物中选择优良性状,使之形态特征适应于农业生产方向进化的过程,因此,大部分种子作物驯化后在落粒性、种子休眠和植株形态等方面都出现了相似的变化。水稻是研究谷类作物驯化的良好模式生物。稻属包含2种栽培稻,分别为亚洲栽培稻(Oryza sativa L.)和非洲栽培稻(O. glaberrima Steud.),其中亚洲栽培稻遍布全世界,包含两个主要亚种,粳稻亚种(O. sativa L. ssp. japonica)和籼稻亚种(O. sativa L. ssp. indica)。稻属丰富的近缘种和广泛的地域分布非常有利于研究确定现代栽培稻的驯化地域。此外,水稻基因组较小、具高质量精细图谱,加上功能基因研究上的进展,也为深入开展水稻驯化进程研究奠定了基础。详见本期第XX-XX页区树俊,汪鸿儒,储成才“亚洲栽培稻主要驯化性状研究进展”,对水稻关键驯化性状研究进行的比较全面的综述。封面图中央是选取23株AA基因组的亚洲栽培稻及其近缘野生稻,利用水稻驯化过程中受到选择的控制稻壳颜色基因Bh4上下游各50 kb中的SNP位点所构建的进化树;图外从左下至右下沿顺时针方向,反映的是水稻驯化过程中稻壳颜色、谷粒形状、穗型的变化趋势。 区树俊,汪鸿儒,储成才（绘图：区树俊）     

Arthropod diversity and community composition on wild and cultivated rice

• 1 Most crop plants are grown far from their region of origin and have been significantly altered by human selection. Given the importance of biodiversity in ecosystem function, surprisingly little is known about the effect of domestication on arthropod diversity and community composition.
• 2 Arthropod diversity and species abundance were compared with three genotypes of cultivated rice Oryza sativa L. and two genotypes of wild rice O. rufipogon Griff. in southern Luzon, the Philippines.
• 3 Domestication had a small but positive effect on total arthropod diversity. Arthropod species richness was highest on the cultivar IR64 and lowest on one of the O. rufipogon genotypes, although arthropod community composition was similar across rice genotypes.
• 4 Total arthropod abundance and the relative abundance of guilds did not differ between wild and cultivated rice. All common herbivores, however, responded to rice domestication. Stem‐boring moths and several sap‐sucking herbivores benefited from domestication, although domestication reduced densities of the wolf spider Pardosa pseudoannulata Boesenberg et Strand.
• 5 By contrast to previous assumptions, crop domestication may not always decrease arthropod diversity. We did not detect any changes in biodiversity or community composition suggesting that rice domestication has altered the capacity of the arthropod community to regulate herbivores.

     

Single-seeded InDel fingerprints in rice:An effective tool for indica-japonica rice classification and evolutionary studies

Asian cultivated rice(Oryza sativa L.),an important cereal crop worldwide,was domesticated from its wild ancestor 8000 years ago.During its long-term cultivation and evolution under diverse agroecological conditions, Asian cultivated rice has differentiated into indica and japonica subspecies.An effective method is required to identify rice germplasm for its indica and japonica features,which is essential in rice genetic improvements.We developed a protocol that combined DNA extraction from a single rice seed and the insertion/deletion(InDel) molecular fingerprint to determine the indica and japonica features of rice germplasm.We analyzed a set of rice germplasm,including 166 Asian rice varieties,two African rice varieties,30 accessions of wild rice species,and 42 weedy rice accessions,using the single-seeded InDel fingerprints(SSIF).The results show that the SSIF method can efficiently determine the indica and japonica features of the rice germplasm.Further analyses revealed significant indica and japonica differentiation in most Asian rice varieties and weedy rice accessions.In contrast,African rice varieties and nearly all the wild rice accessions did not exhibit such differentiation.The pattern of cultivated and wild rice samples illustrated by the SSIF supports our previous hypothesis that indica and japonica differentiation occurred after rice domestication under different agroecological conditions.In addition,the divergent pattern of rice cultivars and weedy rice accessions suggests the possibility of an endoferal origin(from crop)of the weedy rice included in the present study.     

Seeing red: the origin of grain pigmentation in US weedy rice

Weedy forms of crop species infest agricultural fields worldwide and are a leading cause of crop losses, yet little is known about how these weeds evolve. Red rice (Oryza sativa), a major weed of cultivated rice fields in the US, is recognized by the dark‐pigmented grain that gives it its common name. Studies using neutral molecular markers have indicated a close relationship between US red rice and domesticated rice, suggesting that the weed may have originated through reversion of domesticated rice to a feral form. We have tested this reversion hypothesis by examining molecular variation at Rc, the regulatory gene responsible for grain pigmentation differences between domesticated and wild rice. Loss‐of‐function mutations at Rc account for the absence of proanthocyanidin pigments in cultivated rice grains, and the major rc domestication allele has been shown to be capable of spontaneous reversion to a functional form through additional mutations at the Rc locus. Using a diverse sample of 156 weedy, domesticated and wild Oryzas, we analysed DNA sequence variation at Rc and its surrounding 4 Mb genomic region. We find that reversion of domestication alleles does not account for the pigmented grains of weed accessions; moreover, we find that haplotypes characterizing the weed are either absent or very rare in cultivated rice. Sequences from genomic regions flanking Rc are consistent with a genomic footprint of the rc selective sweep in cultivated rice, and they are compatible with a close relationship of red rice to Asian Oryzas that have never been cultivated in the US.     

Genetic analysis of rice domestication syndrome with the wild annual species, Oryza nivara

With a small and sequenced genome, rice provides an excellent system for studying the genetics of cereal domestication. We conducted a quantitative trait locus (QTL) analysis of key domestication traits using an F2 population derived from a cross between the cultivated rice, Oryza sativa, and the annual wild species, O. nivara. We found that the QTL of large phenotypic effects were targeted by domestication selection for effective harvest and planting, including a reduction in seed shattering and seed dormancy and the synchronization of seed maturation. Selection for higher yield was probably responsible for the fixation of mutations at a cluster of QTL on chromosome 7 and a few other chromosomal locations that could have substantially improved plant architecture and panicle structure, resulting in fewer erect tillers and longer and more highly branched panicles in cultivated rice. In comparison with the wild perennial species, O. rufipogon, rice domestication from O. nivara would have involved QTL with a greater degree of chromosomal co-localization and required little genetic change associated with life history or mating system transitions. The genetic analyses of domestication traits with both wild relatives will open opportunities for the improvement of rice cultivars utilizing natural germplasm.     

Molecular Evolution of the TAC1 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(TACl) as a major quantitative trait locus that controls rice tiller angle.To further clarify the evolutionary characterization of the TACl 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 TACl coding regions of the cultivated rice varieties, whereas one synonymous and one nonsynonymous SNP were detected among the TACl coding regions of wild rice accessions.These data indicate that little natural mutation and modification in the TACl coding region occurred within the cultivated rice and its progenitor during evolution.Nucleotide diversities in the TACl gene regions of O.sativa and O.rufipogon of 0.00116 and 0.00112,respectively, further indicate that TACl has been highly conserved during the course of rice domestication.A functional nucleotide polymorphism (FNP) of TACl was only found in the japonica rice group.A neutrality test revealed strong selection,especially in the 3’-flanking region of the TACl 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 TACl sequence analysis suggests that the indica and japonica subspecies arose independently during the domestication of wild rice.     

Evolutionary trajectory of phytoalexin biosynthetic gene clusters in rice

Plants frequently possess operon‐like gene clusters for specialized metabolism. Cultivated rice, Oryza sativa, produces antimicrobial diterpene phytoalexins represented by phytocassanes and momilactones, and the majority of their biosynthetic genes are clustered on chromosomes 2 and 4, respectively. These labdane‐related diterpene phytoalexins are biosynthesized from geranylgeranyl diphosphate via ent‐copalyl diphosphate or syn‐copalyl diphosphate. The two gene clusters consist of genes encoding diterpene synthases and chemical‐modification enzymes including P450s. In contrast, genes for the biosynthesis of gibberellins, which are labdane‐related phytohormones, are scattered throughout the rice genome similar to other plant genomes. The mechanism of operon‐like gene cluster formation remains undefined despite previous studies in other plant species. Here we show an evolutionary insight into the rice gene clusters by a comparison with wild Oryza species. Comparative genomics and biochemical studies using wild rice species from the AA genome lineage, including Oryza barthii, Oryza glumaepatula, Oryza meridionalis and the progenitor of Asian cultivated rice Oryza rufipogon indicate that gene clustering for biosynthesis of momilactones and phytocassanes had already been accomplished before the domestication of rice. Similar studies using the species Oryza punctata from the BB genome lineage, the distant FF genome lineage species Oryza brachyantha and an outgroup species Leersia perrieri suggest that the phytocassane biosynthetic gene cluster was present in the common ancestor of the Oryza species despite the different locations, directions and numbers of their member genes. However, the momilactone biosynthetic gene cluster evolved within Oryza before the divergence of the BB genome via assembly of ancestral genes.     

Sequence polymorphisms in wild,weedy, and cultivated rice suggest seed‐shattering locus sh4 played a minor role in Asian rice domestication

The predominant view regarding Asian rice domestication is that the initial origin of nonshattering involved a single gene of large effect, specifically, the sh4 locus via the evolutionary replacement of a dominant allele for shattering with a recessive allele for reduced shattering. Data have accumulated to challenge this hypothesis. Specifically, a few studies have reported occasional seed‐shattering plants from populations of the wild progenitor of cultivated rice (Oryza rufipogon complex) being homozygous for the putative “nonshattering” sh4 alleles. We tested the sh4 hypothesis for the domestication of cultivated rice by obtaining genotypes and phenotypes for a diverse set of samples of wild, weedy, and cultivated rice accessions. The cultivars were fixed for the putative “nonshattering” allele and nonshattering phenotype, but wild rice accessions are highly polymorphic for the putative “nonshattering” allele (frequency ~26%) with shattering phenotype. All weedy rice accessions are the “nonshattering” genotype at the sh4 locus but with shattering phenotype. These data challenge the widely accepted hypothesis that a single nucleotide mutation (“G”/“T”) of the sh4 locus is the major driving force for rice domestication. Instead, we hypothesize that unidentified shattering loci are responsible for the initial domestication of cultivated rice through reduced seed shattering.     

云南景洪直立型普通野生稻抗稻瘟病Pi-ta+等位基因的克隆与分析

用PCR法从景洪直立紫杆普通野生稻中克隆了抗稻瘟病基因Pi-ta⁺ 的4 672 bp序列, 该序列包含完整的编码框、内含子和终止密码子下游的331 bp。所克隆的直立型紫杆普通野生稻Pi-ta基因序列的编码区与已报道的日本栽培稻社糯(Yashiro-mochi)和元江普通野生稻相应序列间的同源性分别为99.86%和98.78%。与社糯的Pi-ta基因相比, 其编码区有4个核苷酸的差异并导致3个氨基酸残基的改变, 而内含子区域有6个核苷酸差异。对该序列进一步分析发现, 其推导的氨基酸残基的918位为丙氨酸, 属于稀有的抗稻瘟病的Pi-ta⁺ 等位基因。景洪直立型普通野生稻Pi-ta⁺ 基因因其编码序列和推导的氨基酸序列与社糯有所不同, 推测其抗病能力大小和抗菌谱可能与社糯的Pi-ta基因不同。直立型普通野生稻中Pi-ta⁺ 等位基因的克隆为进一步利用该基因改良栽培稻抗病能力提供了前期物质基础。     

The role of Bh4 in parallel evolution of hull colour in domesticated and weedy rice

The two independent domestication events in the genus Oryza that led to African and Asian rice offer an extremely useful system for studying the genetic basis of parallel evolution. This system is also characterized by parallel de‐domestication events, with two genetically distinct weedy rice biotypes in the US derived from the Asian domesticate. One important trait that has been altered by rice domestication and de‐domestication is hull colour. The wild progenitors of the two cultivated rice species have predominantly black‐coloured hulls, as does one of the two U.S. weed biotypes; both cultivated species and one of the US weedy biotypes are characterized by straw‐coloured hulls. Using Black hull 4 (Bh4) as a hull colour candidate gene, we examined DNA sequence variation at this locus to study the parallel evolution of hull colour variation in the domesticated and weedy rice system. We find that independent Bh4‐coding mutations have arisen in African and Asian rice that are correlated with the straw hull phenotype, suggesting that the same gene is responsible for parallel trait evolution. For the U.S. weeds, Bh4 haplotype sequences support current hypotheses on the phylogenetic relationship between the two biotypes and domesticated Asian rice; straw hull weeds are most similar to indica crops, and black hull weeds are most similar to aus crops. Tests for selection indicate that Asian crops and straw hull weeds deviate from neutrality at this gene, suggesting possible selection on Bh4 during both rice domestication and de‐domestication.     

Genetic control of domestication traits in pearl millet (Pennisetum glaucum L., Poaceae)

Quantitative trait loci (QTLs) controlling the morphological differences between pearl millet (Pennisetum glaucum ssp. glaucum) and its wild ancestor (Pennisetum glaucum ssp. monodii, form mollissimum) were investigated in a cultivated/wild F₂ population by means of RFLP markers. The most critical adaptive changes resulting from the domestication process involved the spikelet structure: non-shedding seeds with reduced bracts and bristles and long involucral pedicel. Major differences also concerned characters describing the plant architecture, phenology and spike sizes. Many morphological differences could be attributed to the effect of a small number of loci with relatively large effects. These loci are mainly concentrated on four linkage groups (2, 5, 6 and 7). The loss of shedding ability, due to the absence of a functional abscission layer, is controlled by a single locus on linkage group 6 (al6). Genetic control of the other spikelet traits involved factors with large effects which are located in the region of linkage group 6 close to al6 and to an esterase gene, Esterase-E. Moreover, QTLs with large effects on plant and spike morphology traits such as plant height, number of spikes and weight of the spike were also mapped on linkage groups 6 and 7. This strong linkage of factors in the domestication syndrome may be involved in the maintenance of the phenotypic identity of wild and cultivated populations in sympatry. This result also brings new arguments in the understanding of the domestication process of this allogamous crop. Received: 8 March 1999 / Accepted: 29 April 1999     

Genetic Variation and Evolution of the <Emphasis Type="Italic">Pi9</Emphasis> Blast Resistance Locus in the AA Genome <Emphasis Type="Italic">Oryza</Emphasis> Species

The rice nucleotide-binding site–leucine-rich repeat (NBS-LRR)-encoding resistance (R) gene Pi9 confers broad-spectrum resistance to the fungal pathogen Magnaporthe oryzae. The Pi9 locus comprises many NBS-LRR-like genes and is an ancient locus that is highly conserved in cultivated and wild rice species. To understand the genetic variation and molecular evolutionary mechanism of the Pi9 alleles in different rice species, we studied five AA genome Oryza species including two cultivated rice species (Oryza sativa and Oryza glaberrima) and three wild rice species (Oryza nivara, Oryza rufipogon, and Oryza barthii). A 2.9-kb fragment spanning the NBS-LRR core region of the Pi9 gene was amplified and sequenced from 40 accessions. Sequence comparison revealed that the Pi9 alleles had an intermediate-diversified nucleotide polymorphism among the AA genome Oryza species. Sequence variations were more abundant in the LRR region than in the NBS region, indicating that the LRR region has played a more important role for the evolution of the Pi9 alleles. Furthermore, positive selection was found to be the main force promoting the divergence of the Pi9 alleles, especially in the LRR region. Our results reveal the characteristics and evolutionary dynamics of the Pi9 alleles among the two cultivated and three wild rice species.     

The complex history of the domestication of rice

BACKGROUND: Rice has been found in archaeological sites dating to 8000 bc, although the date of rice domestication is a matter of continuing debate. Two species of domesticated rice, Oryza sativa (Asian) and Oryza glaberrima (African) are grown globally. Numerous traits separate wild and domesticated rices including changes in: pericarp colour, dormancy, shattering, panicle architecture, tiller number, mating type and number and size of seeds. SCOPE: Genetic studies using diverse methodologies have uncovered a deep population structure within domesticated rice. Two main groups, the indica and japonica subspecies, have been identified with several subpopulations existing within each group. The antiquity of the divide has been estimated at more than 100 000 years ago. This date far precedes domestication, supporting independent domestications of indica and japonica from pre-differentiated pools of the wild ancestor. Crosses between subspecies display sterility and segregate for domestication traits, indicating that different populations are fixed for different networks of alleles conditioning these traits. Numerous domestication QTLs have been identified in crosses between the subspecies and in crosses between wild and domesticated accessions of rice. Many of the QTLs cluster in the same genomic regions, suggesting that a single gene with pleiotropic effects or that closely linked clusters of genes underlie these QTL. Recently, several domestication loci have been cloned from rice, including the gene controlling pericarp colour and two loci for shattering. The distribution and evolutionary history of these genes gives insight into the domestication process and the relationship between the subspecies. CONCLUSIONS: The evolutionary history of rice is complex, but recent work has shed light on the genetics of the transition from wild (O. rufipogon and O. nivara) to domesticated (O. sativa) rice. The types of genes involved and the geographic and genetic distribution of alleles will allow scientists to better understand our ancestors and breed better rice for our descendents.     

Life‐history traits and geographical divergence in wild rice (Oryza rufipogon) gene pool in Indochina Peninsula region

Indochina Peninsula is the primary centre of diversity of rice and lies partly in the centre of origin of cultivated rice (Oryza sativa) where the wild ancestor (Oryza rufipogon) is still abundant. The wild gene pool is potentially endangered by urbanisation and the expansion of agriculture, and by introgression hybridisation with locally cultivated rice varieties. To determine genetic diversity and structure of the wild rice of the region we genotyped nearly 1000 individuals using 20 microsatellite loci. We found ecological differentiation in 48 populations, distinguishable by their life‐history traits and the country of origin. Geographical divergence was suggested by isolation of the perennial Myanmar populations from those of Cambodia, Laos and Thailand. The annual types would be most likely to have lost genetic variation because of genetic drift and inbreeding. The growing of cultivated and wild rice together, however, gives ample opportunities for hybridisation, which already shows signs of genetic mixing, and will ultimately lead to replacement of the original wild rice gene pool. For conservation we suggest that wild rice should be conserved ex situ in order to prevent introgression from cultivated rice, along with in situ conservation in individual countries for the recurrent evolutionary process through local adaptation, but with sufficient isolation from cultivated rice fields to preserve genetic integrity of the wild populations.