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.     

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.     

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.     

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.     

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.     

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.     

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.     

<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.

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.     

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.     

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.     

Salt tolerance in <Emphasis Type="Italic">Zea mays</Emphasis> (L). following inoculation with <Emphasis Type="Italic">Rhizobium</Emphasis> and <Emphasis Type="Italic">Pseudomonas</Emphasis>

This study aimed to investigate the effect of inoculation with plant growth-promoting Rhizobium and Pseudomonas species on NaCl-affected maize. Two cultivars of maize (cv. Agaiti 2002 and cv. Av 4001) selected on the basis of their yield potential were grown in pots outdoors under natural conditions during July. Microorganisms were applied at seedling stage and salt stress was induced 21 days after sowing and maintained up to 50% flowering after 120 days of stress. The salt treatment caused a detrimental effect on growth and development of plants. Co-inoculation resulted in some positive adaptative responses of maize plants under salinity. The salt tolerance from inoculation was generally mediated by decreases in electrolyte leakage and in osmotic potential, an increase in osmoregulant (proline) production, maintenance of relative water content of leaves, and selective uptake of K ions. Generally, the microbial strain acted synergistically. However, under unstressed conditions, Rhizobium was more effective than Pseudomonas but under salt stress the favorable effect was observed even if some exceptions were also observed. The maize cv. Agaiti 2002 appeared to be more responsive to inoculation and was relatively less tolerant to salt compared to that of cv. Av 4001.     

<Emphasis Type="Italic">Calamintha nepeta</Emphasis> (L.) Savi and <Emphasis Type="Italic">Micromeria thymifolia</Emphasis> (Scop.) Fritsch cultivated in Italy

Calamintha nepeta and Micromeria thymifolia have been traditionally used in the Mediterranean area as condiments and medicinal plants for a long time. Whereas in parts of Italy C. nepeta (special recipes have been developed in Lazio and Tuscany) is also an established garden plant showing different evolutionary products and their interaction among each other and the wild progenitor, M. thymifolia is being developed into a new crop plant. Both plants and their uses are described with regard to Italy. There is a marked tendency to broaden the use of condiments and spices which results in new crop plants which have to be documented and elaborated in further studies. Many species of Labiatae are predisposed to use by man and new items can be found even in areas which have to be considered as well studied.     

A significant proportion of indigenous rhizobia from India associated with soybean (<Emphasis Type="Italic">Glycine max</Emphasis> L.) distinctly belong to <Emphasis Type="Italic">Bradyrhizobium</Emphasis> and <Emphasis Type="Italic">Ensifer</Emphasis> genera

The diversity among 269 rhizobia isolated from naturally occurring root nodules of soybean collected from two different agro-ecological regions of India, based on RFLP and sequences of the intergenic spacer (IGS) between the 16S and 23S rRNA genes, growth rate, and indole acetic acid production, revealed their significant, site-dependent genomic diversity. Among these bacteria, nine IGS genotypes were identified with two endonucleases. They were distributed into five divergent lineages by sequence analysis of each IGS representative strain, i.e., (1) comprising IGS genotypes I, II, III, and reference Bradyrhizobium yuanmingense; (2) with genotype IV and strains of unclassified bradyrhizobia genomic species; (3) including genotypes V, VI, and Bradyrhizobium liaoningense; (4) with IGS genotype VII and Bradyrhizobium elkanii strains; and (5) comprising IGS genotypes VIII, IX, and different Ensifer genus bacteria. Host-specificity test revealed that all rhizobia-nodulated soybean and cowpea and only part of them formed nodules on Arachis hypogeae and Cajanus cajan. The great diversity of soybean nodulators observed in this study emphasises that Indian soil is an important reservoir of nitrogen-fixing rhizobia.     

<Emphasis Type="Italic">Rhizobium</Emphasis>,<Emphasis Type="Italic"> Bradyrhizobium</Emphasis> and<Emphasis Type="Italic"> Agrobacterium</Emphasis> strains isolated from cultivated legumes

The present study was conducted to isolate and characterize rhizobial strains from root nodules of cultivated legumes, i.e. chickpea, mungbean, pea and siratro. Preliminary characterization of these isolates was done on the basis of plant infectivity test, acetylene reduction assay, C-source utilization, phosphate solubilization, phytohormones and polysaccharide production. The plant infectivity test and acetylene reduction assay showed effective root nodule formation by all the isolates on their respective hosts, except for chickpea isolate Ca-18 that failed to infect its original host. All strains showed homology to a typical Rhizobium strain on the basis of growth pattern, C-source utilization and polysaccharide production. The strain Ca-18 was characterized by its phosphate solubilization and indole acetic acid (IAA) production. The genetic relationship of the six rhizobial strains was carried out by random amplified polymorphic DNA (RAPD) including a reference strain of Bradyrhizobium japonicum TAL-102. Analysis conducted with 60 primers discriminated between the strains of Rhizobium and Bradyrhizobium in two different clusters. One of the primers, OPB-5, yielded a unique RAPD pattern for the six strains and well discriminated the non-nodulating chickpea isolate Ca-18 from all the other nodulating rhizobial strains. Isolate Ca-18 showed the least homology of 15% and 18% with Rhizobium and Bradyrhizobium, respectively, and was probably not a (Brady)rhizobium strain. Partial 16S rRNA gene sequence analysis for MN-S, TAL-102 and Ca-18 strains showed 97% homology between MN-S and TAL-102 strains, supporting the view that they were strains of B. japonicum species. The non-infective isolate Ca-18 was 67% different from the other two strains and probably was an Agrobacterium strain.     

Putative Role of <Emphasis Type="Italic">Flavobacterium</Emphasis>, <Emphasis Type="Italic">Dokdonella</Emphasis> and <Emphasis Type="Italic">Methylophilus</Emphasis> Strains in Paracetamol Biodegradation

Paracetamol, the most widely and globally used analgesic and antipyretic, is easily accumulated in aquatic environments. In the present study, the biodegradation of paracetamol in different media (one for general growth, one specific for sulfate reducing bacteria, a mineral salts medium and municipal wastewater) inoculated with two types of sludge (from anaerobic lagoon and from oxidation ditch) under different oxygenic conditions (anoxic; moderate oxygenation in open flasks and high oxygenation by aeration) was investigated. In addition, bacteria with relative abundances increasing simultaneously with paracetamol degradation, when this drug was the only carbon source, thus with a putative role in its degradation, were identified using 16S rRNA gene sequences. The results show that aerobic microorganisms had a major role in the degradation of paracetamol, with 50 mg/L totally removed from municipal wastewater after 2 days incubation with aeration, and that the metabolites 4-aminophenol and hydroquinone plus one compound not identified in this work were produced in the process. The identification of bacteria with a role in the degradation of paracetamol revealed a strain from genus Pseudomonas with the highest final relative abundance of 21.2%, confirming previous works reporting strains of this genus as paracetamol decomposers. Besides, genera Flavobacterium, Dokdonella and Methylophilus were also in evidence, with initial relative abundances of 1.66%, 1.48 and 0.00% (not detected) in the inoculum and 6.91%, 3.80 and 3.83% after incubation, respectively. Therefore, a putative role of these genera in paracetamol biodegradation is suggested for the first time.

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Graphical Abstract ?

     

Crossability of <Emphasis Type="Italic">Vigna rhomboidea</Emphasis> Burtt. Davy with Cowpea (<Emphasis Type="Italic">V. unguiculata</Emphasis> (L.) Walp.)

V. rhomboidea is a wild Vigna species that is a potential source of genes for pubescence which could be incorporated into cultivated cowpea for insect pests resistance. Due to the lack of reliable records on the crossability and gene pool relationships between V. rhomboidea and cowpea, crossing trials were conducted in the screenhouse to observe if V. rhomboidea is reciprocally crossable (compatible) with cowpea. Crossability of V. rhomboidea (as seed parent) with cowpea (as pollen parent) was, for the first time, successfully achieved at the rate of 5.7% from 1145 crosses. Reciprocal crosses with cowpea as seed parent and V. rhomboidea pollen parent gave an average of 22.6% pod set from 2299 crosses. It is concluded that V. rhomboidea is reciprocally compatible with cowpea. This implies that V. rhomboidea belongs to the primary gene pool of cowpea.