The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication

The extent of molecular differentiation between domesticated animals or plants and their wild relatives is postulated to be small. The availability of the complete genome sequences of two subspecies of the Asian rice, Oryza sativa (indica and japonica) and their wild relatives have provided an unprecedented opportunity to study divergence following domestication. We observed significantly more amino acid substitutions during rice domestication than can be expected from a comparison among wild species. This excess is disproportionately larger for the more radical kinds of amino acid changes (e.g. Cys<-->Tyr). We estimate that approximately a quarter of the amino acid differences between rice cultivars are deleterious, not accountable by the relaxation of selective constraints. This excess is negatively correlated with the rate of recombination, suggesting that 'hitchhiking' has occurred. We hypothesize that during domestication artificial selection increased the frequency of many deleterious mutations.     

Migration, isolation and hybridization in island crop populations: the case of Madagascar rice

Understanding how crop species spread and are introduced to new areas provides insights into the nature of species range expansions. The domesticated species Oryza sativa or Asian rice is one of the key domesticated crop species in the world. The island of Madagascar off the coast of East Africa was one of the last major Old World areas of introduction of rice after the domestication of this crop species and before extensive historical global trade in this crop. Asian rice was introduced in Madagascar from India, the Malay Peninsula and Indonesia approximately 800-1400 years ago. Studies of domestication traits characteristic of the two independently domesticated Asian rice subspecies, indica and tropical japonica, suggest two major waves of migrations into Madagascar. A population genetic analysis of rice in Madagascar using sequence data from 53 gene fragments provided insights into the dynamics of island founder events during the expansion of a crop species' geographic range and introduction to novel agro-ecological environments. We observed a significant decrease in genetic diversity in rice from Madagascar when compared to those in Asia, likely the result of a bottleneck on the island. We also found a high frequency of a unique indica type in Madagascar that shows clear population differentiation from most of the sampled Asian landraces, as well as differential exchange of alleles between Asia and Madagascar populations of the tropical japonica subspecies. Finally, despite partial reproductive isolation between japonica and indica, there was evidence of indica/japonica recombination resulting from their hybridization on the island.     

The Rc and Rd genes are involved in proanthocyanidin synthesis in rice pericarp

Different colors, such as purple, brown, red and white, occur in the pericarp of rice. Here, two genes affecting proanthocyanidin synthesis in red- and brown-colored rice were elucidated. Genetic segregation analysis suggested that the Rd and A loci are identical, and both encode dihydroflavonol-4-reductase (DFR). The introduction of the DFR gene into an Rcrd mutant resulted in red-colored rice, which was brown in the original mutant, demonstrating that the Rd locus encodes the DFR protein. Accumulation of proanthocyanidins was observed in the transformants by the introduction of the Rd gene into the rice Rcrd line. Protein blot analysis showed that the DFR gene was translated in seeds with alternative translation initiation. A search for the Rc gene, which encodes a transacting regulatory factor, was conducted using available DNA markers and the Rice Genome Automated Annotation System program. Three candidate genes were identified and cloned from a rice RcRd line and subsequently introduced into a rice rcrd line. Brown-colored seeds were obtained from transgenic plants by the introduction of a gene containing the basic helix-loop-helix (bHLH) motif, demonstrating that the Rc gene encodes a bHLH protein. Comparison of the Rc locus among rice accessions showed that a 14-bp deletion occurred only in the rc locus.     

Independent domestication of Asian rice followed by gene flow from japonica to indica

Results from studies on the domestication process of Asian rice Oryza sativa have been controversial because of its complicated evolutionary history. Previous studies have yielded two alternative hypotheses about the origin(s) of the two major groups of O. sativa: japonica and indica. One study proposes a single common wild ancestor, whereas the other suggests that there were multiple domestication events of different types of wild rice. Here, we provide clear evidence of the independent domestication of japonica and indica obtained via high-throughput sequencing and a large-scale comparative analysis of two wild rice accessions (W1943 and W0106) and two cultivars (a japonica cultivar called "Nipponbare" and an indica cultivar called "Guangluai-4"). The different domestication processes of the two cultivar groups appear to have led to distinct patterns of molecular evolution in protein-coding regions. The intensity of purifying selection was relaxed only in the japonica group, possibly because of a bottleneck effect. Moreover, a genome-wide comparison between Nipponbare, Guangluai-4, and another indica cultivar (93-11) suggests multiple hybridization events between japonica and indica, both before and after the divergence of the indica cultivars. We found that a large amount of genomic DNA, including domestication-related genes, was transferred from japonica to indica, which might have been important in the development of modern rice. Our study provides an overview of the dynamic process of Asian rice domestication, including independent domestication events and subsequent gene flow.     

Origins of functional nucleotide polymorphisms in a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice

qLTG3-1 is a major quantitative trait locus (QTL) controlling tolerance to low-temperature at the seed germination stage (termed low-temperature germinability) in rice using a population derived from the cross between Italica Livorno from Italy and Hayamasari from Japan. Map-based cloning identified that qLTG3-1 encodes a protein of unknown function. The molecular identification of this major QTL could make it possible to identify allelic variation and favorable alleles for rice breeding programs. The present study examined the identification of qLTG3-1 alleles and their distribution among 62 landraces of Asian cultivated rice (Oryza sativa L.) collected from 19 different countries, termed the rice core collection. In the coding region, a single non-synonymous substitution and 3 in-frame insertion/deletion polymorphisms (indels) were detected. The almost completely conserved protein alignment of qLTG3-1 was also identified among 5 Oryza species, suggesting that the function of qLTG3-1 is critical for seed germination or for rice growth by pleiotropic effects of the gene. The functional nucleotide polymorphisms (FNPs), a 71-bp deletion found in Hayamasari and an amino acid substitution found in Nipponbare, was identified in varieties from Japan. These alleles with FNPs might be adapted to rice cultivation in specific local conditions. The present results may contribute to the utilization of favorable alleles of qLTG3-1 for the improvement of low-temperature germinability in rice breeding programs.     

Association between nonsynonymous mutations of starch synthase IIa and starch quality in rice (Oryza sativa)

Starch quality is one of the most important agronomic traits in Asian rice, Oryza sativa. Starch synthase IIa (SsIIa) is a major candidate gene for starch quality variation. Within SsIIa, three nonsynonymous mutations in exon 8 have been shown to affect enzyme activity when expressed in Escherichia coli. To search for the variation in SsIIa that is responsible for starch quality variation in rice, we sequenced the SsIIa exon 8 region and measured starch quality as starch disintegration in alkali for 289 accessions of cultivated rice and 57 accessions of its wild ancestor, Oryza rufipogon. A general linear model and nested clade analysis were used to identify the associations between the three nonsynonymous single nucleotide polymorphisms (SNPs) and starch quality. Among the three nonsynonymous SNPs, we found strong evidence of association at one nucleotide site ('SNP 3'), corresponding to a Leu/Phe replacement at codon 781. A second SNP, corresponding to a Val/Met replacement at codon 737, could potentially show an association with increased sample sizes. Variation in SsIIa enzyme activity is associated with the cohesiveness of rice grains when cooked, and our findings are consistent with selection for more cohesive grains during the domestication of tropical japonica rice.     

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）     

Genome-wide haplotype changes produced by artificial selection during modern rice breeding in Japan

During the last 90 years, the breeding of rice has delivered cultivars with improved agronomic and economic characteristics. Crossing of different lines and successive artificial selection of progeny based on their phenotypes have changed the chromosomal constitution of the ancestors of modern rice; however, the nature of these changes is unclear. The recent accumulation of data for genome-wide single-nucleotide polymorphisms (SNPs) in rice has allowed us to investigate the change in haplotype structure and composition. To assess the impact of these changes during modern breeding, we studied 177 Japanese rice accessions, which were categorized into three groups: landraces, improved cultivars developed from 1931 to 1974 (the early breeding phase), and improved cultivars developed from 1975 to 2005 (the late breeding phase). Phylogenetic tree and structure analysis indicated genetic differentiation between non-irrigated (upland) and irrigated (lowland) rice groups as well as genetic structuring within the irrigated rice group that corresponded to the existence of three subgroups. Pedigree analysis revealed that a limited number of landraces and cultivars was used for breeding at the beginning of the period of systematic breeding and that 11 landraces accounted for 70% of the ancestors of the modern improved cultivars. The values for linkage disequilibrium estimated from SNP alleles and the haplotype diversity determined from consecutive alleles in five-SNP windows indicated that haplotype blocks became less diverse over time as a result of the breeding process. A decrease in haplotype diversity, caused by a reduced number of polymorphisms in the haplotype blocks, was observed in several chromosomal regions. However, our results also indicate that new haplotype polymorphisms have been generated across the genome during the breeding process. These findings will facilitate our understanding of the association between particular haplotypes and desirable phenotypes in modern Japanese rice cultivars.     

Comprehensive profiling and natural variation of flavonoids in rice

Flavonoids constitute a major group of plant phenolic compounds. While extensively studied in Arabidopsis, profiling and natural y occurring variation of these compounds in rice (Oryza sativa), the mon...     

Selection under domestication: evidence for a sweep in the rice waxy genomic region

Rice (Oryza sativa) was cultivated by Asian Neolithic farmers >11,000 years ago, and different cultures have selected for divergent starch qualities in the rice grain during and after the domestication process. An intron 1 splice donor site mutation of the Waxy gene is responsible for the absence of amylose in glutinous rice varieties. This mutation appears to have also played an important role in the origin of low amylose, nonglutinous temperate japonica rice varieties, which form a primary component of Northeast Asian cuisines. Waxy DNA sequence analyses indicate that the splice donor mutation is prevalent in temperate japonica rice varieties, but rare or absent in tropical japonica, indica, aus, and aromatic varieties. Sequence analysis across a 500-kb genomic region centered on Waxy reveals patterns consistent with a selective sweep in the temperate japonicas associated with the mutation. The size of the selective sweep (>250 kb) indicates very strong selection in this region, with an inferred selection coefficient that is higher than similar estimates from maize domestication genes or wild species. These findings demonstrate that selection pressures associated with crop domestication regimes can exceed by one to two orders of magnitude those observed for genes under even strong selection in natural systems.     

The molecular bases of cereal domestication and the history of rice

In this review, we discuss the development of molecular genetics and genomics that has allowed one to identify and characterize some of the key genes involved in cereal domestication. The list is far from being complete, but the first conclusion that can be drawn from the published works is that only a few loci have been the target of human selection in the first stages of the domestication process at the late neolithic. Mutations at these few loci have led to dramatic changes in plant morphology and phenology, transforming a wild into a cultivated plant. We also show that in the case of rice, for which the complete genome sequence is available, the development of new molecular markers based on retrotransposon insertion polymorphisms helped to resolve some of the questions regarding the origin of the domestication of the crop in Asia. To cite this article: O. Panaud, C. R. Biologies 332 (2009).     

中国粳稻地方品种孕穗期耐冷性评价及聚类分析

用原产于中国18个省的329份粳稻地方品种为材料,分析了自然低温和冷水胁迫下不同省份粳稻地方品种孕穗期耐冷性及主要农艺性状表型差异和聚类特点。结果表明,在自然低温和冷水胁迫下各省份粳稻地方品种的孕穗期耐冷性状及主要农艺性状有明显的差异。在自然低温和冷水胁迫下,天津、四川和台湾品种的结实率及冷水反应指数均较高,表现较强的孕穗期耐冷性和迟钝的冷水反应。云南品种在自然低温下表现为较强的孕穗期耐冷性（结实率）,而在冷水胁迫下播种至抽穗天数和株高的冷水反应指数较高,表现为迟钝的冷水反应。从总体趋势上看,自然低温和冷水胁迫下,除个别省份外,纬度相对较高的北方省份品种的孕穗期耐冷性（结实率）强于纬度相对较低的南方省份品种。此外,在自然低温和冷水胁迫下,各省粳稻地方品种的聚类结果总体上与各省品种的地理位置及其耐冷性有密切的联系,而在冷水胁迫下品种的聚类结果与品种地理位置的关系比自然低温下更为密切。     

Nonindependent domestication of the two rice subspecies, Oryza sativa ssp. indica and ssp. japonica, demonstrated by multilocus microsatellites

The origins of the Asian cultivated rice Oryza sativa from its wild ancestor O. rufipogon have been debated for decades. The question mainly concerns whether it originated monophyletically or polyphyletically. To shed light on the origins and demographic history of rice domestication, we genotyped a total of 92 individual plants from the two O. sativa subspecies and O. rufipogon for 60 microsatellites. An approximate Bayesian method was applied to estimate demographic parameters for O. rufipogon vs. O. sativa ssp. indica and O. rufipogon vs. O. sativa ssp. japonica. We showed that the japonica subspecies suffered a more severe bottleneck than the indica subspecies and thus a greater loss of genetic variation during its domestication. Across microsatellite loci there is a significant positive correlation in the reduction of genetic diversity between the two subspecies. The results suggest that completely independent domestication of indica and japonica subspecies may not explain our data and that there is at least partial sharing of their ancestral populations and/or recent gene flow between them.     

云南地方稻核心种质耐低磷特性研究

1引言磷是作物的必需性营养元素,人类将面临农业可持续发展与磷素资源严重短缺的矛盾[17].土壤普查结果表明,全国有59%以上的土壤缺磷[1].为了提高作物产量,生产中通过施用磷肥来解决土壤缺磷的问题.由于磷肥利用率低,不仅增加生产成本,还带来资源短缺、环境污染及食品安全等诸多问题[21,26].发掘水稻利用磷的内在潜力,培育磷高效利用新品种,可减少磷的施用量.近年来,野生或地方稻绿色基因发掘及改良进展显著,如资源高效利用[22~24]、高产基因[3,20,27]和抗性基因[2,13]等,利用植物基因型间磷元素利用效率的差异,筛选和培育磷高效基因型作物…     

Two evolutionary histories in the genome of rice: the roles of domestication genes

Genealogical patterns in different genomic regions may be different due to the joint influence of gene flow and selection. The existence of two subspecies of cultivated rice provides a unique opportunity for analyzing these effects during domestication. We chose 66 accessions from the three rice taxa (about 22 each from Oryza sativa indica, O. sativa japonica, and O. rufipogon) for whole-genome sequencing. In the search for the signature of selection, we focus on low diversity regions (LDRs) shared by both cultivars. We found that the genealogical histories of these overlapping LDRs are distinct from the genomic background. While indica and japonica genomes generally appear to be of independent origin, many overlapping LDRs may have originated only once, as a result of selection and subsequent introgression. Interestingly, many such LDRs contain only one candidate gene of rice domestication, and several known domestication genes have indeed been "rediscovered" by this approach. In summary, we identified 13 additional candidate genes of domestication.     

Natural selection in gene-dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice

Levels of nucleotide variability are frequently positively correlated with recombination rate and negatively associated with gene density due to the effects of selection on linked variation. These relationships are determined by properties that frequently differ among species, including the mating system, and aspects of genome organization such as how genes are distributed along chromosomes. In rice, genes are found at highest density in regions with frequent crossing-over. This association between gene density and recombination rate provides an opportunity to evaluate the effects of selection in a genomic context that differs from other model organisms. Using single-nucleotide polymorphism data from Asian domesticated rice Oryza sativa ssp. japonica and ssp. indica and their progenitor species O. rufipogon, we observe a significant negative association between levels of polymorphism and both gene and coding site density, but either no association, or a negative correlation, between nucleotide variability and recombination rate. We establish that these patterns are unlikely to be explained by neutral mutation rate biases and demonstrate that a model of background selection with variable rates of deleterious mutation is sufficient to account for the gene density effect in O. rufipogon. In O. sativa ssp. japonica, we report a strong negative correlation between polymorphism and recombination rate and greater losses of variation during domestication in the euchromatic chromosome arms than heterochromatin. This is consistent with Hill-Robertson interference in low-recombination regions, which may limit the efficacy of selection for domestication traits. Our results suggest that the physical distribution of selected mutations is a primary factor that determines the genomic pattern of polymorphism in wild and domesticated rice species.     

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。     

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.