In an effort to identify the geographical locations of different domestication events, Londo et al. While conclusions drawn from a sample of three genes cannot be considered definitive, the data show an association between japonica -like haplotypes and wild accessions from China and indica -like haplotypes and wild accessions collected across the Himalayan Mountains in Thailand, India and neighbouring countries.
Interestingly, some domesticated japonicas do not share a haplotype with any O. This work suggests the subspecies separation was enforced by significant geographical barriers in addition to the genetic sterility barriers. Many researches have made crosses between O. These studies have shown that domestication traits are influenced by many different loci. Several researchers have noted that QTLs for domestication traits tend to cluster within certain regions of the rice genome.
The centromere region of chromosome 7 is the site of QTLs for seed colour, panicle structure, dormancy and shattering, among others Xiong et al. Other clusters for domestication traits have been reported on rice chromosomes 3, 4, 6, 8, 9, 11 and 12 Cai and Morishima, ; Li et al. This positional convergence may represent clusters of domestication loci, or possibly major domestication genes with pleiotrophic effects on many traits.
Based on the previously presented evidence of independent domestications for indica and japonica we would expect that different suites of genes and corresponding mutations influencing domestication traits would have been selected within the different subspecies or subpopulations.
Therefore, when crosses are made between the two subspecies, the offspring should segregate for wild alleles at several loci and wild characteristics should re-appear among sub-specific populations. This has, in fact, been observed. Most notably for traits like dormancy and shattering, intra-specific crosses between parents with low dormancy and shattering give rise to progeny that have higher levels of dormancy and shattering than either parent Lin et al.
However, levels of dormancy and shattering in these crosses are not as high as wild accessions, suggesting either that indica and japonica share some domestication alleles or that independent mutations within the same domestication loci occurred in each subspecies which fail to compliment when crossed. Another confirmation that different domestication genes were under selection in different subpopulations comes from QTL studies.
Populations derived from crosses between a single wild accession and diverse cultivars often identity different QTLs for domestication traits Xiao et al. The large number of resources currently available to rice researches, not the least of which is genome sequence from representatives of both japonica Nipponbare and indica 93—11 cultivars Goff et al.
Recently several groups have reported the cloning of genes influencing traits associated with the domestication syndrome. Two of these papers report the cloning of genes affecting shattering. The first of these papers looked at a cross between the wild species O. QTL analysis of the F 2 progeny from this cross identified three genomic regions affecting shattering. The effect of the locus was so great that a single allele caused all mature grain on the panicle to drop when the panicle was simply tapped, while the absence of this allele required shaking to induce shattering.
Fine mapping identified the gene underlying this QTL as a Myb transcription factor and association and transformation studies pinpointed the functional nucleotide polymorphism FNP to a single base pair within the DNA binding domain of this gene. The non-shattering allele was also found in several non-shattering accessions of O.
These accessions most likely represent outcrosses with domesticated plants that transferred the non-shattering allele back into the wild germplasm, as the non-shattering wild plants which were selected and further modified by human selections would have faced strong negative selective pressures in the wild.
Curiously, the non-shattering allele was present in all the O. If in fact the domestications of the indica and japonica subspecies were completely independent, we might expect mutations at the same locus, but would not expect to see the same functional polymorphisms at domestication loci.
It is highly unlikely that the same SNP would independently arise in both subspecies, and the likelihood decreases dramatically when we consider the fact that all O. Independent mutations occurring in different genetic backgrounds would be expected to carry different signature haplotypes across the target region. The fact that both the FNP and the corresponding haplotypes were identical in both indica and japonica cultivars at the sh4 locus provides strong evidence for the conclusion that the allele arose once and then crossed the geographic and genetic barriers that divide the two subspecies.
Why the allele for non-shattering and not the non-shattering plants themselves was dispersed is an interesting puzzle, suggesting that early farmers were selecting for the non-shattering trait in combination with additional traits not found in the original non-shattering plants.
Cloning other domestication genes and tracing their evolutionary history and patterns of distribution will allow us to determine whether introgression across subspecies is a common occurrence in the domestication of rice, or an isolated case for sh4. It is possible that one subspecies was domesticated and subsequently was crossed to local wild rices as it was carried to new locations.
Heavy natural and artificial selective pressures combined with loss of progeny due to intra-specific sterility barriers between the indica and japonica genomes would give rise to plants that resembled the locally adapted wild species but that contained a few valuable introgressions harbouring domestication genes from the new introductions. Alternatively, domestication events in the subspecies may have been truly independent and when the early domesticates were grown in close proximity, they crossed.
Beneficial alleles with a clear advantage were thus transferred and would have been the targets of selection by early agriculturalists. Despite a fixed sh4 allele within O. Traditionally, indicas have been reported to have higher shattering levels than japonicas and, as mentioned above, crosses between indica and japonica display transgressive segregation for shattering Konishi et al.
This suggests that shattering alleles at loci other than sh4 are differentially fixed within each of the two populations. The second group to clone a shattering gene worked with a cross between the aus variety, Kasalath, and the temperate japonica variety, Nipponbare Konishi et al. Fine mapping pinpointed the FNP to an SNP 12 kb upstream of a BEL1-type homeobox gene and the function of this promoter polymorphism was confirmed using transformation.
In situ hybridization demonstrated that this change in the promoter region eliminated the expression of the homeobox gene at the provisional abscission layer without changing expression of the gene elsewhere. Within the isoline carrying the Nipponbare qSH1 allele in a Kasalath background, the lack of qSH1 gene expression in this tissue results in the complete lack of an abscission layer.
Screening the varieties within temperate japonica showed an association between this allele and levels of shattering but also demonstrated that selection for the qSH1 allele was not as intense nor as expansive as selection for the sh4 allele, as qSH1 is not fixed, even within the temperate japonica subpopulation, let alone the whole of O. A third domestication gene that was recently cloned is the Rc gene which confers a red pericarp Sweeney et al.
Red pericarp colour is ubiquitous in wild populations where it confers resistance to various biotic stresses. Early landraces are red; however, modern cultivars are almost universally white. While red-grained varieties are still preferred in some places due to traditional or medicinal reasons, white rice has been under strong selection for thousands of years.
Unlike shattering, which is clearly a polygenic trait, only one locus, Rc , has been reported to affect a change from red pericarp to white.
This locus was positionally cloned from a cross between O. Using a combination of fine mapping and sequence analysis of multiple alleles, Sweeney et al.
The gene's function is impaired in the Jefferson cultivar by a bp frame-shift deletion that truncates the protein before the bHLH domain. While association studies examining the prevalence of this mutation among white rices throughout O. Either the recessive allele leading to white pericarp is common within O. By tracing the origin of the alleles of domestication genes and the paths they travelled to achieve their current distribution, we gain fresh insights into the history of human interactions, a history that was not recorded but is written in the genomes of the plants we selected and upon which we have come to depend.
We thank Lisa Polewczak for the photographs of rice plants and Lois Swales for administrative help. National Center for Biotechnology Information , U. Journal List Ann Bot v. Ann Bot. Published online Jul 6. Author information Article notes Copyright and License information Disclaimer. E-mail ude. This article has been cited by other articles in PMC. Abstract Background Rice has been found in archaeological sites dating to bc , although the date of rice domestication is a matter of continuing debate.
Scope Genetic studies using diverse methodologies have uncovered a deep population structure within domesticated rice. Conclusions The evolutionary history of rice is complex, but recent work has shed light on the genetics of the transition from wild O. Key words: Oryza sativa , domestication, shattering, pericarp colour, QTL, subpopulation structure, subspecies.
Open in a separate window. QTLs between wild and domesticated Many researches have made crosses between O. Domestication genes that have been cloned The large number of resources currently available to rice researches, not the least of which is genome sequence from representatives of both japonica Nipponbare and indica 93—11 cultivars Goff et al.
Archaeology, languages, and the African past. Lanham: Alta Mira Press: Heredity and genetic mapping of domestication-related traits in a temperate japonica weedy rice.
Theoretical and Applied Genetics. QTL clusters reflect character associations in wild and cultivated rice. Ancient paddy soils from the Neolithic age in China's Yangtze river delta. The archaeology of ancient China.
Origin, evolution, cultivation, dissemination, and diversification of Asian and African rices. Polyphyletic origin of cultivated rice based on the interspersion pattern of SINEs. Molecular Biology and Evolution. The origins of rice agriculture: recent progress in East Asia. La riziculture en Afique occidentale. Annales de Geographie. Philippine Agricultural Scientist.
Agricultural origins and frontiers in South Asia: a working synthesis. Journal of World Prehistory. Contrasting patterns in crop domestication and domestication rates: recent archaeobotanical insights from the Old World. Other rice remains which have used to infer domestication, such as phytoliths-including a fan shaped type from the leaves and a two-peaked type from the rice husk-are equally uncertain for determining whether rice was domesticated, but show tendencies towards directional change over time where measurements have been made.
Luckily, as discussed below, new methods It is also the case that early Chinese sites with rice finds also produced evidence for quantities of definitely wild foods, such as acorns, Trapa water chestnuts, and another marsh nut of Asia, Euryale ferox. Proponents of a hypothesis of later domestication including member of the Early Rice Project contend that this find indicates a predominantly hunter-gatherer-fisher lifestyle, and that only with later cultivation and domestication of rice, perhaps closer to BC, did people give up gathering as many nuts and focus on farming rice.
This raises the need to consider not just the evidence of rice remains themselves but to systematically study rice in the relation to an overall picture of plant use reflect in archaeobotanical assemblages. Strong evidence for a slow domestication process, which indeed finished late, were published in Science in BP of rice domestication in China: a response. Holocene African rice has been cultivated for years. Between and BC, Oryza glaberrima propagated from its original centre, the Niger River delta, and extended to Senegal.
However, it never developed far from its original region. Its cultivation even declined in favour of the Asian species, which was introduced to East Africa early in the common era and spread westward.
African rice helped Africa conquer its famine of Rice was grown in some areas of southern Iraq. With the rise of Islam it moved north to Nisibin, the southern shores of the Caspian Sea and then beyond the Muslim world into the valley of Volga. In Egypt , rice is mainly grown in the Nile Delta. In Palestine, rice came to be grown in the Jordan Valley. Rice is also grown in Yemen. The Moors brought Asiatic rice to the Iberian Peninsula in the 10th century. Records indicate it was grown in Valencia and Majorca.
In Majorca, rice cultivation seems to have stopped after the Christian conquest, although historians are not certain. Muslims also brought rice to Sicily, where it was an important crop long before it is noted in the plain of Pisa or in the Lombard plain , where its cultivation was promoted by Ludovico Sforza, Duke of Milan, and demonstrated in his model farms.
After the 15th century, rice spread throughout Italy and then France , later propagating to all the continents during the age of European exploration. The Ottomans introduced rice to the Balkans. Rice is not native to the Americas but was introduced to Latin America and the Caribbean by European colonizers at an early date with Spanish colonizers introducing Asian rice to Mexico in the s at Veracruz and the Portuguese and their African slaves introducing it at about the same time to Colonial Brazil.
Recent scholarship suggests that enslaved Africans played an active role in the establishment of rice in the New World and that African rice was an important crop from an early period.
Varieties of rice and bean dishes that were a staple dish along the peoples of West Africa remained a staple among their descendants subjected to slavery in the Spanish New World colonies, Brazil and elsewhere in the Americas. The Native Americans of what is now the Eastern United States may have practiced extensive agriculture with forms of wild rice. References to wild rice in the Americas are to the unrelated Zizania palustris.
From the enslaved Africans, plantation owners learned how to dyke the marshes and periodically flood the fields. At first the rice was milled by hand with wooden paddles, then winnowed in sweetgrass baskets the making of which was another skill brought by slaves from Africa. The invention of the rice mill increased profitability of the crop, and the addition of water power for the mills in by millwright Jonathan Lucas was another step forward.
Rice culture in the southeastern U. Today, people can visit the only remaining rice plantation in South Carolina that still has the original winnowing barn and rice mill from the midth century at the historic Mansfield Plantation in Georgetown, South Carolina.
The predominant strain of rice in the Carolinas was from Africa and was known as "Carolina Gold. In the southern United States, rice has been grown in southern Arkansas, Louisiana, and east Texas since the midth century.
Many Cajun farmers grew rice in wet marshes and low lying prairies where they could also farm crawfish when the fields were flooded. In recent years rice production has risen in North America, especially in the Mississippi River Delta areas in the states of Arkansas and Mississippi.
Rice cultivation began in California during the California Gold Rush, when an estimated 40, Chinese laborers immigrated to the state and grew small amounts of the grain for their own consumption. However, commercial production began only in in the town of Richvale in Butte County.
By , California produced the second largest rice crop in the United States, after Arkansas, with production concentrated in six counties north of Sacramento.
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