Origin of rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) domestication genes

A number of genes that contribute to the domestication traits of cultivated rice have been identified. These include Sh4, Rc, PROG1 and LABA1, which are associated with non-shattering rachis, white pericarp, erect growth and barbless awns, respectively. The mutations giving rise to the “domestication alleles” of these genes are either invariable in cultivated rice, or have variability that is strictly associated with the phenotypic trait. This observation forms the basis to those current rice domestication models that envisage a single origin for the domesticated phenotype. Such models assume that the domestication alleles are absent or rare in wild rice, emerged under cultivation and spread across all rice groups by introgressive hybridization. We examined whole-genome sequencing datasets for wild and cultivated rice to test the former two assumptions. We found that the rc and laba1 alleles occur in wild rice with broad geographical distribution, and reach frequencies as high as 13 and 15%, respectively. These results are in agreement with previous observations of the prog1 and sh4 domestication alleles in wild populations. We also show that the diversity of the genomic regions surrounding the rc, laba1, prog1 and sh4 alleles in wild accessions is greater than that in cultivated rice, suggesting that these alleles emerged prior to domestication. Our findings indicate that the possibility that independent rice groups obtained identical domestication alleles directly from the wild population needs to be considered.     

Assessment of artificial selection in maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) and Asian rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) using QTL data

Maize (Zea mays L.) and Asian rice (Oryza sativa L.), two most important cereals for human nutrition, have undergone strong artificial selection during a long period of time. Currently, a number of genes with stronger signals of selection have been identified through combining genomic and population genetic approach, but research on artificial selection of maize and Asian rice is scarcely done from the perspective of phenotypic difference of a number of agronomic traits. In this study, such an investigation was carried out on the basis of 179 published studies about phenotypic quantitative trait locus (QTL) mapping of Zea and Oryza species via QTL sign test. At the overall level, the proportions of antagonistic QTLs of Zea and Oryza species were 0.2446 and 0.2382 respectively, deviating significantly from neutrality. It indicated that these two genera have undergone similar selection strength during their evolutionary process. A previous study showed that 4 traits undergoing the directional selection during domestication were identified in Asian rice via QTL sign test, and 16 individual traits in Asian rice and 38 ones in maize that newly detected in this study deviated significantly from neutrality as well, demonstrating the dominant influence of artificial selection on them. Moreover, analysis of different categories of cross type including O. sativa × Oryza rufipogon (perennial and annual forms) crosses, maize × teosinte (Zea mays subsp. parviglumis) crosses, O. sativa × O. sativa crosses, and maize × maize crosses showed that their proportions of antagonistic QTLs were 0.1869, 0.1467, 0.2649, and 0.2618 respectively. These results revealed that selection strength of domestication is significantly stronger than that of modern genetic improvement. However, interestingly, the proportion of antagonistic QTLs (0.1591) in maize × maize with long-term selection was very similar to that (0.1467) in the maize × teosinte (Zea mays subsp. parviglumis) crosses. It suggested that some favorable traits could be cultivated within a few decades if we carry out strong selection. In addition, the proportions of antagonistic QTLs of the widely cultivated hybrids of rice (Minghui 63 × Zhenshan 97) and maize (Zheng 58 × Chang 7-2) in China were 0.309 and 0.3472 respectively. It suggested that selection during modern genetic improvement has significantly acted on them.     

Genetic diversity of cultivated rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) and wild rice (<Emphasis Type="Italic">Oryza rufipogon</Emphasis> Griff.) in Asia,especially in Myanmar,as revealed by organelle markers

Asian rice (Oryza sativa L.) is widely cultivated in Asia, where it has been classified into Indica and Japonica Group, the latter is further classified into Tropical and Temperate Japonica Subgroup. O. rufipogon is believed to be the closest ancestor to O. sativa, but it remains unclear whether the two groups arose from a single ancestor or different ancestors. Therefore, here, we investigated the matrilineal ancestors of O. sativa using markers for organelle (chloroplast and mitochondrial) genomes, and 119 O. sativa landraces, 10 O. glaberrima Steud., 115 O. rufipogon Griff. from Asia, and 39 accessions from other wild rice species with AA genomes. We screened 18 organelle markers developed based on polymorphic loci in the organelle genomes. In addition, we used the open reading frame 100 of a chloroplast marker. The results indicated that O. rufipogon first differentiated into two lineages and then further differentiated into Indica and Japonica Group, respectively. Accessions of O. rufipogon (R-1f and R-2d types) from Myanmar appear to be the closest ancestors of Tropical Japonica Subgroup and Indica Group, respectively. Therefore, these wild strains may have made a strong contribution to the domestication of rice landraces in Myanmar.     

Effects of phosphate on trace element accumulation in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.): a 5-year phosphate application study

Purpose

Phosphate (P) fertilizers are being widely used to increase crop yield, especially in P-deficient soils. However, repeated applications of P could influence trace element bioaccumulation in crops. The effects of 5-year P enrichment on trace element (Cu, Zn, Cd, Pb, As, and Hg) accumulation in Oryza sativa L. were thus examined.

Materials and methods

Two paddy soils with different initial P availabilities were amended with and without P fertilizer from 2009 to 2013. Trace elements and P levels in rice and soils were analyzed.

Results and discussion

In soil initially with limited P, P amendment enhanced grain Pb, As, and Hg concentrations by 1.8, 1.5, and 1.4-fold, respectively, but tended to decrease the grain Cd level by 0.73-fold, as compared to the control. However, in soil initially with sufficient P, P amendment tended to reduce accumulation of all examined elements in rice grain.

Conclusions

Phosphate amendment in initially P-limited and P-sufficient soils had different effects on trace element availability in soil (as reflected by extractable element) and plant physiology (growth and metal translocation), resulting in contrasting patterns of trace element accumulation in rice between the two types of soils. Our study emphasized the necessity to consider the promoting effects of P on Pb, As, and Hg accumulation in grain in initial P-deprived soil.

     

Shattering or not shattering: that is the question in domestication of rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

The loss of shattering of rice has long been acknowledged as a crucial step sweeping the path of domestication. Here, we collated evidence from genetics, and anthropology to challenge this long-held view. Our discussion dwelt on arguments that (1) undermined the effect of a mutation in the key locus (sh4) which does not always confer non-shattering, (2) identified the involvement of other loci, (3) uncovered natural variation in shatterability still existing in domesticated landraces, and (4) relatively recent fixation of the mutation. Similarly, cultural attributes asserted a long tradition of naturally shattering wild rice cultivation and adaptive strategies of gathering which is still widely exercised in many parts of South and South-East Asia, Africa, and Australia. Altogether, it strongly suggests that primitive agriculture thrived largely relying on wild rice or semi-domesticated shattering phenotype but non-shattering emerged into conspicuity much later in the history.     

Variation of floral traits in Thai rice germplasm (<Emphasis Type="Italic">Oryza sativa</Emphasis>)

Floral traits play an important role in mating systems in flowering plant species. In rice, variation in floral traits has been established in a wide range of germplasm, but the variability of floral traits in Thai rice remains uncharacterized. Sixty-seven rice varieties that are cultivated throughout the country and two accessions of common wild rice were evaluated for nine floral traits to assess the extent of variation, and the differentiation of floral traits among groups of rice (improved rice varieties, selected traditional varieties, local traditional varieties and wild rice). The range of variation of all traits examined in Thai rice varied within the extent of variation that has been reported in other rice germplasm. Most of the floral traits observed in Thai rice have mean values similar to other reports, except in stamen traits, percentage of stigma exertion and the length of spikelet, which exhibited higher mean values than other germplasm investigations. Since these floral traits have a large contribution on outcrossing potential, Thai rice might have a greater chance of natural outcrossing compared to other cultivated rice germplasm. There is no clear differentiation in floral traits among groups of cultivated rice, but there are obvious differences in most of the floral traits between cultivated rice varieties and common wild rice, illustrated in the transformation of rice floral structures during domestication. The results have implications for outcrossing and spontaneous gene flow as well as a potential use in the parental lines for hybrid rice seed production.     

Diversity and differentiation of <Emphasis Type="Italic">Oryza sativa</Emphasis> and <Emphasis Type="Italic">O. rufipogon</Emphasis> in Indonesia

Analysis of the genetic structure of Indonesian Oryza sativa and O. rufipogon using neighbour-joining trees based on single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers revealed that O. sativa in Indonesia is separated from O. rufipogon. Accessions of O. sativa in this study were differentiated into two major groups, indica and tropical japonica, excluding some varieties. SSR and SNP markers revealed the high value of differentiation (F _ST) and genetic distance (D) between indica and tropical japonica and we discovered four loci by SNP markers and one locus by SSR markers that play a role in differentiation between indica and tropical japonica. Interestingly, genetic diversity (H) in O. rufipogon was lower than that in O. sativa, however H in O. rufipogon was the highest and H in tropical japonica was the lowest when O. sativa was divided into two groups. Inbreeding coefficient (Fst) showed evidences that gene flow (Nm) between species and within species might be one of the mechanisms related to the diversification and differentiation of Indonesian rice germplasm by asymmetric pattern between species and within O. sativa as revealed by SSR and SNP markers. In addition, we found evidences on stabilizing selection in Indonesian rice germplasm and they might be the reasons why Indonesian rice germplasm did not differentiate due to source location of landrace. However, we found a weak relation between SSR and SNP markers probably due to highly polymorphic in SSR and the different properties of both markers.     

Morpho-agronomic and simple sequence repeat-based diversity in colored rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) germplasm from peninsular India

Knowledge of the genetic diversity in the germplasm accessions is important for the efficient germplasm management. We studied 45 colored rice accessions, which had been earlier collected from peninsular India. The accessions were evaluated at two diverse locations for 12 morpho-agronomic traits and genotyped using 50 simple sequence repeat (SSR) markers. Significant genotypic variability was observed for all morpho-agronomic traits studied. Dendrogram and principal component analysis based on morpho-agronomic traits separated the accessions into three clusters. The first two principal components accounted for 82% of the total variation. The most discriminatory traits were number of grains per panicle, biomass yield, and days to flowering and maturity. The SSR analysis revealed high polymorphic information content value of 0.84. Though, Mantel test did not show a significant correlation, yet the classification based on phenotyping and genotyping data showed good agreement for the expression of morpho-agronomic traits in the formation of clusters. Five accessions had high concentration (> 100 μg/g) of Fe and one of Zn. Our study revealed the presence of large genetic variation among the colored rice accessions evaluated and moderate agreement between morpho-agronomic and SSR–based classifications and of these with geographic diversity.     

Arsenic,cadmium, and lead pollution and uptake by rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) grown in greenhouse

Purpose  

Hunan province is well-known for its extensive base-metal extraction and smelting industries. However, the legacies of excavation operations, transportation, and selective smelting activities within Hunan have resulted in the generation of large quantities of mine wastes, which will become the sources of metal contamination in the environment. Thus, there is an increasingly important health issue underlying the study of arable land pollution and transfer of As, Cd, and Pb in the paddy soil–rice system.     

The dynamics of spatial and temporal population genetic structure of weedy rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> f. <Emphasis Type="Italic">spontanea</Emphasis> Baker)

Weedy rice (Oryza sativa f. spontanea Baker) is one of the most serious weeds in direct-seeded rice production; adversely affecting rice areas and yield in Thailand. The objectives of this study were to evaluate the level of morphological and agronomical variation and the level and pattern of genetic diversity and population structure of weedy rice populations in Thailand. Sixty-three weedy rice populations collected from three rice production areas of Thailand were sampled over four rice cultivation seasons to study phenotypic characteristics, genetic diversity and population structure. All analysis included comparison with seven cultivated rice varieties and seven local common wild rice populations. The results demonstrated considerable genetic and morphological variation, population structure, and changing dynamics of Thai weedy rice populations, both within and between regions and growing seasons. Phenotypic and genotypic variations and population structure of weedy rice populations changed temporally, with a trend over five years toward greater similarity to companion crop rice varieties. The ongoing gene flow, combined with ecological conditions created by farmers’ selection and agronomic practices, may enhance fitness and adaptability of weedy rice populations and stimulate the evolution of invasiveness in weedy rice plants. The adaptive evolution of weedy rice tended to parallel cultivated rice for high adaptation to the agronomic practices, possibly including selection for crop mimicry, which has led to the convergence of weedy populations phenotypically and genetically with the companion crop rice.     

Coleoptile length of barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.) cultivars

Coleoptile length is related to maximum seeding depth. The coleoptile length of 44 spring barley cultivars (Hordeum vulgare L.) was determined by laying seeds on moistened filter paper and incubating at 15°C for 13 days. Significant differences in coleoptile length were noted between cultivars (P < 0.05). Most cultivars had a coleoptile length between 60 and 80 mm. Five cultivars (Buloke, Dash, Harrington, Morrell and Tallon) had a coleoptile length shorter than 60 mm. Seven cultivars (CM72, Doolup, Finniss, Fleet, Hannan, Haruna Nijo and Macumba) had a coleoptile length longer than 80 mm. No relationship was found between early growth habit or plant height and coleoptile length. The impact of different dwarfing genes on coleoptile length was discussed. Differences in coleoptile length observed should be exploited by breeders to improve the tolerance of barley to deep seeding and stubble retention. This would be a useful tool in managing climate variability and would assist barley growers to sow closer to the optimum sowing time in situations where moisture is present at depth but not on the soil surface.     

Identification of <Emphasis Type="Italic">SUB1A</Emphasis> alleles from wild rice <Emphasis Type="Italic">Oryza rufipogon</Emphasis> Griff.

Submergence stress is a major constraint to rice production in South and Southeast Asia. Most rice (Oryza sativa L.) cultivars die within a week of complete submergence, while a small number of accessions are submergence-tolerant for up to 2 weeks or more. These cultivars have the tolerant allele of the SUB1A gene, one of three ERF genes at this locus on rice chromosome 9. In all O. sativa varieties studied, the SUB1A gene is limited to a subset of indica accessions of O. sativa. Thus far, there has been no published report of the SUB1A gene in wild rice species. Here we report evidence of the SUB1A gene found in wild species of O. rufipogon Griff. accessions by the use of degenerate primers corresponding to the most highly conserved regions of the SUB1 locus. The results indicated that two SUB1A-like alleles, e.g. OrSub1A-1 and OrSub1A-2, were identified from two O. rufipogon accessions. Submergence treatment shows that both of the accessions with SUB1A-like genes were submergence-intolerant. This preliminary study provides insight into the origin and allelic variation of SUB1A, an agronomically important gene that is rapidly being introduced into widely-grown rice cultivars.     

Morphological diversity of panicle traits in Kam fragrant glutinous rice (<Emphasis Type="Italic">Oryza sativa</Emphasis>)

Panicle traits are the most intuitive and representative features of rice germplasm resources that have been utilized in the determination of its identity, genetic diversity, yield, and quality. Based on the approaches of ethnobotany, cultural anthropology and plant morphology, we analyzed the panicle traits of 95 traditional Kam fragrant glutinous rice landraces according to folk classification in Qiandongnan Prefecture of Guizhou Province in the past 10 years. A total of 95 Kam fragrant glutinous rice landraces were tested, of which 91% consisted of those with awns, and landraces with awn lengths of 2–6 cm comprised 62%. The coefficient of variation (CV) of awn color, husk color and Grain color was more than 50%, thereby indicating extensive morphological variations among the traditional Kam fragrant glutinous rice landraces. The average Shannon–Wiener value (diversity index, H′) for panicle qualitative traits was 0.50, which was significantly higher than that of quantitative traits (0.22), thereby indicating a relatively higher degree of genetic diversity among qualitative traits. Cluster analysis of panicle morphological traits showed that 95 Kam fragrant glutinous rice landraces could be divided into five categories, using the Euclidean distance of 0.68 as threshold. Each cultivar manifested unique panicle traits. The present study on the morphological diversity of Kam fragrant glutinous rice landraces provided basic information that may be utilized for the conservation and sustainable use of Kam fragrant glutinous rice landraces.     

Comparison of morphological traits and molecular markers to analyse diversity and structure of alfalfa (<Emphasis Type="Italic">Medicago sativa</Emphasis> L.) cultivars

Diversity and structure of populations may differ substantially between morphological traits and molecular markers. Explanations of such discrepancies are crucial for further progress in breeding as well as for the maintenance of genetic resources. Our objective was to compare indices of among-cultivars differentiation for morphological traits (Q_ST) and molecular markers (F_ST) in alfalfa (Medicago sativa), a legume forage species. Ten cultivars representing the Northern and Southern types commonly grown in Europe were investigated. For each cultivar, 40 genotypes were analysed with 16 SSR markers and four morphological traits measured in two locations and several cuts. Q_ST values were in general high (0.02–0.39) compared to the differentiation observed with molecular markers (F_ST = 0.01), especially for growth habit, indicating that morphological traits were more efficient to structure the diversity than molecular markers. For morphological traits, a clear separation of Northern and Southern cultivars was observed, whereas for molecular markers, no clear structure was detected. Nevertheless, the grazing type cultivar Luzelle was separated from the rest of the cultivars for both morphological traits and molecular markers. Although pairwise differences between cultivars were significant for both morphological traits and molecular markers, the main part of the variation was found within cultivars. This large within-cultivar variation may be explained, besides the outcrossing reproductive mode and autotetraploid genetics, by the recent history of M. sativa domestication in Europe and the frequent seed exchanges. Selection for morphological traits (Q_ST > F_ST) was achieved without modification of within-cultivar neutral diversity.     

Response of flooded rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) to nitrogen application at two root-zone temperature regimes in a pot experiment

In a greenhouse experiment, the response of three cultivars of rice to N application was studied at two root-zone moisture regimes. The response was measured in terms of dry matter yield, uptake of N from applied fertilizer and soil organic matter, loss of fertilizer N, and interaction of applied N with the native soil N. Nitrogen was applied as ¹⁵N-labelled ammonium sulphate and two temperature regimes in the root-zone were established by digging one set of pots into the soil, while keeping the other set on the surface. This setup created and maintained a temperature difference of 5–7°C in the rhizosphere, temperature being lower in the buried pots throughout the growth period. The rice cultivars included a coarse-grain and high-yielding cultivar (IR-6) and two aromatic fine-grain cultivars (Bas-198 and Bas-Pak). IR-6 showed a negative response to higher root-zone temperature with resultant reduced efficiency of soil N and fertilizer N. The other two cultivars were relatively insensitive. The effect of temperature was more pronounced for N yield than dry matter accumulation. Loss of applied N occurred in all cases, but it was more pronounced in IR-6 at the higher temperature regime. Application of labelled fertilizer N led to an increase in the uptake of unlabelled N due to a real "added nitrogen interaction" which was attributed mainly to an increase in root biomass.     

Soil nematode community varies between rice cultivars but is not affected by transgenic Bt rice expressing <Emphasis Type="Italic">Cry1Ab</Emphasis> or <Emphasis Type="Italic">Cry1Ab</Emphasis>/<Emphasis Type="Italic">Cry1Ac</Emphasis>

Insecticidal crystal (Cry) proteins produced by transgenic Bacillus thuringiensis (Bt) rice that enter the soil via root exudation and plant residues may be harmful to non-target soil organisms. We conducted a 3-year field investigation to determine if soil nematode abundance and diversity were affected by exposure to two transgenic Bt rice cultivars, compared to their non-transgenic near isolines. Near isolines were Kemingdao (KMD-Bt) expressing the single Cry1Ab gene and its non-Bt near isoline Xiushui-11 (XSD), as well as Huahui-1 (HH-Bt) expressing the fused Cry1Ab/Cry1Ac gene and its non-Bt near isoline Minghui-63 (MH). Nematode variables including community composition, abundance, trophic groups, and most of the common genera differed significantly between the rice cultivars. However, these nematode variables were similar under transgenic Bt rice and its non-Bt near isoline, although higher Shannon’s index value and Pielou’s index value were found in soils planted with Bt rice than the non-Bt near isoline. During this 3-year field study, gene modification (single Cry1Ab gene and fused Cry1Ab/Cry1Ac gene) supports a more uniform distribution of nematode species but had no effect on soil nematode abundance and community composition. We conclude that continuous cultivation of KMD-Bt and HH-Bt rice varieties for 3 years is not detrimental to soil nematode communities under field conditions.     

<Emphasis Type="Italic">Ziziphus </Emphasis><Emphasis Type="Italic">spina-christi</Emphasis> (L.) Willd.: a multipurpose fruit tree

Neglected and underutilized species often play a vital role in securing food and livestock feed, income generation and energy needs of rural populations. In spite of their great potential little attention has been given to these species. This increases the possibility of genetic erosion which would further restrict the survival strategies of people in rural areas. Ziziphus spina-christi is a plant species that has edible fruits and a number of other beneficial applications that include the use of leaves as fodder, branches for fencing, wood as fuel, for construction and furniture making, and the utilization of different parts e.g. Fruits, leaves, roots and bark in folk medicine. Moreover, the plant is adapted to dry and hot climates which make it suitable for cultivation in an environment characterized by increasing degradation of land and water resources. Lack of research in Z. spina-christi hinders its successful improvement and promotion. Therefore, studies are needed to fully exploit this species. This article aims at summarizing information on different aspects of Z. spina-christi to stimulate interest in this crop which is of importance in Sudan and other countries of the semi-arid tropics.

Joint toxicity of three plant protection products to <Emphasis Type="Italic">Triticum aestivum</Emphasis> (L.) and <Emphasis Type="Italic">Brassica rapa</Emphasis> (L.)

Purpose  

Few studies have been conducted to evaluate the effects of mixtures of chemicals in terrestrial environment. Thus, it seems important to evaluate if the combined application of pesticides currently used in agricultural fields may pose a risk to terrestrial plants.     

Genetic diversity of European pear cultivars (<Emphasis Type="Italic">Pyrus communis</Emphasis> L.) and wild pear (<Emphasis Type="Italic">Pyrus pyraster</Emphasis> (L.) Burgsd.) inferred from microsatellite markers analysis

The aim of this study was to identify the group of highly polymorphic microsatellite markers for the identification of six pear cultivars (P. communis) and two individuals of wild pear (P. pyraster). From among 40 tested SSR markers, 19 were selected to profile genetic diversity in pear genotypes due to high polymorphisms. These markers showed high heterozygosity levels (0.5–1) and, on average, 6.4 alleles per marker were found. The set of microsatellite markers employed in this study demonstrated usefulness of microsatellite markers for the identification of pear genotypes. The examined wild forms were represented in this study by only two individuals of P. pyraster. It can be assumed that these forms were distinctly different from the cultivated pear cultivars.     

Evidence of N<Subscript>2</Subscript>O emission and gaseous nitrogen losses through nitrification-denitrification induced by rice plants (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

A greenhouse experiment was conducted with a specially designed apparatus consisting of an upper and lower chamber where the treatment with rice was carried out (treatment 1). The apparatus also had a single chamber where treatment 2, without rice plants, was carried out. The scope of this study was to elucidate the influence of rice plant growth on gaseous N losses as N₂ and N₂O produced by nitrification-denitrification in a flooded soil fertilized with (NH₄)₂SO₄ (with 56.50 atom% ¹⁵N). Gas samples were withdrawn weekly and analyzed for (N₂ + N₂O)-¹⁵N losses by mass spectrometer and for N₂O by gas chromatograph. The gaseous (N₂ + N₂O)-¹⁵N losses of the treatment with rice plants were significantly (P =0.01) higher than those of the treatment without rice plants, as were the amounts of N₂O emitted. Rice plants facilitate the efflux of N₂ and N₂O from soil to atmosphere, as about half of the total gaseous ¹⁵N loss as N₂ and N₂O was found in the upper chamber. The proportion of N₂O-¹⁵N to (N₂ + N₂O)-¹⁵N in the upper chamber was 10.56%, much higher than that of the lower chamber in treatment 1 and the headspace of treatment 2.