Allozyme variation and evolutionary relationships of grain amaranths (Amaranthus spp.)

Summary Allozyme studies in amaranth provided useful assays of genetic variation in order to verify the patterns inferred from morphological traits, for elucidating the genetic structure of landraces, and for the studies of evolutionary relationships among wild, weedy and crop species. Thirty-four populations of cultivated New World amaranths were surveyed along with 21 weedy New World populations for allozyme variation at nine electrophoretic enzyme loci. Eleven populations of cultivated amaranths from the Indian State of Uttar Pradesh and six from Nepal were also surveyed for a comparison. In the New World populations, heterozygosity was low, and different populations ranged from 0 to 44% polymorphic loci. Adjacent populations were often fixed for different alleles or had very different allele frequencies at certain loci, with no apparent geographical patterns. Diversity index H was partitioned into the intra- and interpopulation as well as the interspecific components of variability. The crop versus weed genetic distances were the largest, whereas the intra- and interpopulation components of H were about equal. Genetic structure of all three species of the New World amaranths together can be described as a collection of distinct populations, each more or less a heterogeneous collection of highly homozygous individuals. The North Indian populations showed relatively less allozyme variability with the most common alleles same as those of Mexican landraces. Alleles at several loci proved to be diagnostic of the crop and weed groups, and of the three individual crop species. Genetic distances based on pooled gene frequencies showed the three crop species to be generally more closely related inter se than they were to their putative weedy progenitor species, respectively (with the exception of the weed-crop pair A. quitensis and A. caudatus). This implies a single domestication event involving A. hybridus as the common ancestor rather than three separate domestication events. Close similarity between A. caudatus and A. quitensis might have resulted from transdomestication based on a weedy or semi-domesticated species having migrated from Meso-America to South America. This preliminary report must now be expanded by further ecogeographical, cytogenetic and population studies on new extensive collections from the areas of early domestication. Some evidence of recent introgression and/or segregation of crop-weed hybrids between A. caudatus and A. retroflexus is available in the form of rare individuals in crop populations with crop allozyme genotypes except for a single homozygous weedy allele.     

Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia

Weedy rice is a close relative of domesticated rice (Oryza sativa) that competes aggressively with the crop and limits rice productivity worldwide. Most genetic studies of weedy rice have focused on populations in regions where no reproductively compatible wild Oryza species occur (North America, Europe and northern Asia). Here, we examined the population genetics of weedy rice in Malaysia, where wild rice (O. rufipogon) can be found growing in close proximity to cultivated and weedy rice. Using 375 accessions and a combined analysis of 24 neutral SSR loci and two rice domestication genes (sh4, controlling seed shattering, and Bh4, controlling hull colour), we addressed the following questions: (i) What is the relationship of Malaysian weedy rice to domesticated and wild rice, and to weedy rice strains in the USA? (ii) To what extent does the presence of O. rufipogon influence the genetic and phenotypic diversity of Malaysian weeds? (iii) What do the distributions of sh4 and Bh4 alleles and associated phenotypes reveal about the origin and contemporary evolution of Malaysian weedy rice? Our results reveal the following: independent evolutionary origins for Malaysian weeds and US strains, despite their very close phenotypic resemblance; wild‐to‐weed gene flow in Malaysian weed populations, including apparent adaptive introgression of seed‐shattering alleles; and a prominent role for modern Malaysian cultivars in the origin and recent proliferation of Malaysian weeds. These findings suggest that the genetic complexity and adaptability of weedy crop relatives can be profoundly influenced by proximity to reproductively compatible wild and domesticated populations.     

Plant population and weeds influence stalk insects, soil moisture, and yield in rainfed sunflowers

Insect infestation, soil moisture, and yield were examined in populations of≈33 140 plants/ha （low） and ≈ 40 340 plants/ha （high） of an oilseed sunflower, Helianthus annuus L, cv. ＇ Triumph 660CL＇ with two levels of weediness. Less weedy plots resulted from the application of herbicide combination of S-metolachlor and sulfentrazone, whereas more weedy plots resulted from application of sulfentrazone alone. Among the 12 weed species recorded, neither plant numbers nor biomass differed between crop plant densities. Larvae of the stalk-boring insects Cylindrocopturus adspersus （Coleoptera： Curculionidae） and Mordellistena sp. （Coleoptera： Mordellidae） were less abundant in high density sunflowers, ostensibly due to reduced plant size. However, the same effect was not observed for Dectes texanus （Coleoptera： Cerambycidae） or Pelochrista womanana （Lepidoptera： Tortricidae）, two other stalk-boring insects. Soil moisture was highest in low density and lowest in the high density sunflowers that were less weedy. Stalk circumference, head diameter, and seed weight were reduced for sunflower plants with short interplant distances （mean = 20 cm apart） compared to plants with long interplant distances （mean = 46 cm apart）. These three variables were greater in less weedy plots compared with more weedy plot〉 and positively correlated with interplant distance. Yields on a per-hectare basis paralleled those on a per-plant basis but were not different among treatments. The agronomic implications of planting density are discussed in the context of weed and insect management.     

Molecular evolution of shattering loci in U.S. weedy rice

Cultivated rice fields worldwide are plagued with weedy rice, a conspecific weed of cultivated rice (Oryza sativa L.). The persistence of weedy rice has been attributed, in part, to its ability to shatter (disperse) seed prior to crop harvesting. In the United States, separately evolved weedy rice groups have been shown to share genomic identity with exotic domesticated cultivars. Here, we investigate the shattering phenotype in a collection of U.S. weedy rice accessions, as well as wild and cultivated relatives. We find that all U.S. weedy rice groups shatter seeds easily, despite multiple origins, and in contrast to a decrease in shattering ability seen in cultivated groups. We assessed allelic identity and diversity at the major shattering locus, sh4, in weedy rice; we find that all cultivated and weedy rice, regardless of population, share similar haplotypes at sh4, and all contain a single derived mutation associated with decreased seed shattering. Our data constitute the strongest evidence to date of an evolution of weeds from domesticated backgrounds. The combination of a shared cultivar sh4 allele and a highly shattering phenotype, suggests that U.S. weedy rice have re‐acquired the shattering trait after divergence from their progenitors through alternative genetic mechanisms.     

Nutrient levels in corn and competing weed species in a first year milpa,Indian church,Belize, C.A.

Summary Grain production in two 1/4 hectare plots gave 2971 and 1380 kg/ha for an average yield of 2175 kg/ha. Average yield for local farmers was 1700 kg/ha. Weed biomass accounted for 50% of total bioomass in the hydric Site 4, but held 64–83% of the total nutrients. In the mesic Site 1, values were 5% and 3–29% respectively.Canna edulis was the most abundant weed species. Soil nutrient levels neither increased or decreased significantly between clearing and harvesting. Any decline in future crop production would be due to increased weed competition and not a decline in soil fertility. Weevil (Sitophilus zeamais) infestation is a serious problem in hybrid corn not encountered with local varieties.     

Domestication,phylogeny and taxonomic delimitation in underutilized grain Amaranthus (Amaranthaceae) – a status review

Many neglected, underutilized species are extremely important for food production especially in Low Income Food Deficient Countries (LIFDCs). Grain amaranth is one of such crops originated and domesticated in different parts of American continent. Lack of knowledge on taxonomy and phylogenetic relationship with other related crops, analysis of the extent and distribution of genetic diversity together with work on local and traditional knowledge, are the main constrains for genetic improvement of neglected, underutilized and crop related wild species. The phylogenetic relationship and taxonomic delimitation in genus Amaranthus are still not resolved with extreme clarity. But classification of the genus Amaranthus into three subgenera viz., Acnida, Amaranthus and Albersia, based on morphological parameters is quite acceptable. Phylogenetic analysis revealed clear separation of vegetable and grain amaranths. The derivation of grain and vegetable amaranths represent two lines of descent from weed progenitor. Amaranthus hybridus L. along with grain amaranths supposed to have formed a complex in which taxonomic problems are far from being clarified, especially because of apparent common hybridization and misapplication of nomenclature. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Genetic diversity and relationships detected by isozyme and RAPD analysis of crop and wild species of Amaranthus

 Genetic diversity and relationships of 23 cultivated and wild Amaranthus species were examined using both isozyme and RAPD markers. A total of 30 loci encoding 15 enzymes were resolved, and all were polymorphic at the interspecific level. High levels of inter-accessional genetic diversity were found within species, but genetic uniformity was observed within most accessions. In the cultivated grain amaranths (A. caudatus, A. cruentus, and A. hypochondriacus), the mean value of H_T was 0.094, H_S was 0.003, and G_ST was 0.977 at the species level. The corresponding values in their putative wild progenitors (A. hybridus, A. powellii, and A. quitensis) were 0.135, 0.004, and 0.963, respectively. More than 600 RAPD fragments were generated with 27 arbitrary 10-base primers. On average, 39.9% of the RAPD fragments were polymorphic among accessions within each crop species; a similar level of polymorphism (42.8%) was present in the putative progenitors, but much higher levels of polymorphism were found in vegetable (51%) and other wild species (69.5%). The evolutionary relationships between grain amaranths and their putative ancestors were investigated, and both the RAPD and isozyme data sets supported a monophyletic origin of grain amaranths, with A. hybridus as the common ancestor. A complementary approach using information from both isozymes and RAPDs was shown to generate more accurate estimates of genetic diversity, and of relationships within and among crop species and their wild relatives, than either data set alone. Received: 13 March 1997/Accepted: 6 May 1997     

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

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

Nitrate reductase activity,biomass, yield,and quality in cotton in response to nitrogen fertilization

In the production of cotton (Gossypium hirsutum L.), nitrogen fertilization is one of the most costly crop practices, but important to reach high yields. However, high nitrogen (N) content in plants does not always translate into a high fibre production. One way of assessing the efficiency of the N fertilizer is through the enzymatic activity of the nitrate reductase (NR). This is a key enzyme in N assimilation, whose activity is regulated by a number of endogenous and exogenous factors that determine yield. The aim of this study was to assess the effect of N fertilization on yield, fibre quality, biomass, and NR enzymatic activity in vivo in the cotton variety Fiber Max 989. The evaluated application rates were 0, 50, 100, and 150 kg/ha of N, using urea as a source (46% N) in a randomizedblock design with three replicates. At harvest, the maximum yield of seed cotton and the greatest accumulation of total foliar biomass through time was reached after applying 150 kg N/ha. The different N-application rates did not affect the components of cotton-fibre quality. The activity of endogenous NR was greater on plants where 150 kg N/ha were applied. The highest cotton yield and N contents were obtained on these plants. Therefore, the NR activity in vivo could be used as a bioindicator of the N nutritional level in cotton.     

Gene Flow and its Consequences in Sorghum spp.

Gene flow between crops and their weedy or wild relatives can be problematic in modern agricultural systems, especially if it endows novel adaptive genes that confer tolerance to abiotic and biotic stresses. Alternatively, gene flow from weedy relatives to domesticated crops may facilitate ferality through introgression of weedy characteristics in the progeny. Cultivated sorghum (Sorghum bicolor), is particularly vulnerable to the risks associated with gene flow to several weedy relatives, johnsongrass (S. halepense), shattercane (S. bicolor ssp. drummondii) and columbusgrass (S. almum). Johnsongrass and shattercane are common weeds in many sorghum production areas around the world. Sorghum varieties with adaptive traits developed through conventional breeding or novel transgenesis pose agronomic and ecological risks if transferred into weedy/wild relatives. Knowledge of the nature and characteristics of gene flow among different sorghum species is scarce, and existing knowledge is scattered. Here, we review current knowledge of gene flow between cultivated sorghum and its weedy and wild relatives. We further discuss potential avenues for addressing gene flow through genetic, molecular, and field level containment, mitigation and management strategies to facilitate successful deployment of novel traits in this economically important crop species.     

Spatial and Temporal Variation of Roots, Arbuscular Mycorrhizal Fungi, and Plant and Soil Nutrients in a Mature Pinot Noir (Vitis vinifera L.) Vineyard in Oregon, USA

Soil and crop management practices may influence biomass growth and yields of cotton (Gossypium hirsutum L.) and sorghum (Sorghum bicolorL.) and sequester significant amount of atmospheric CO₂in plant biomass and underlying soil, thereby helping to mitigate the undesirable effects of global warming. This study examined the effects of three tillage practices [no-till (NT), strip till (ST), and chisel till (CT)], four cover crops [legume (hairy vetch) (Vicia villosa roth), nonlegume (rye) (Secale cerealeL), hairy vetch/rye mixture, and winter weeds orno covercrop], and three N fertilization rates (0, 60–65, and 120–130 kg N ha ^–1) on the amount of C sequestered in cotton lint (lint + seed), sorghum grain, their stalks (stems + leaves) and roots, and underlying soil from 2000 to 2002 in central Georgia, USA. A field experiment was conducted on a Dothan sandy loam (fine-loamy, kaolinitic, thermic, Plinthic Kandiudults). In 2000, C accumulation in cotton lint was greater in NT with rye or vetch/rye mixture but in stalks, it was greater in ST with vetch or vetch/rye mixture than in CT with or without cover crops. Similarly, C accumulation in lint was greater in NT with 60 kg N ha ^–1 but in stalks, it was greater in ST with 60 and 120 kg N ha ^–1 than in CT with 0 kg N ha ^–1. In 2001, C accumulation in sorghum grains and stalks was greater in vetch and vetch/rye mixture with or without N rate than in rye without N rate. In 2002, C accumulation in cotton lint was greater in CT with or without N rate but in stalks, it was greater in ST with 60 and 120 kg N ha ^–1 than in NT with or without N rate. Total C accumulation in the above- and belowground biomass in cotton ranged from 1.7 to 5.6 Mg ha ^–1 and in sorghum ranged from 3.4 to 7.2 Mg ha ^–1. Carbon accumulation in cotton and sorghum roots ranged from 1 to 14% of the total C accumulation in above- and belowground biomass. In NT, soil organic C at 0–10 cm depth was greater in vetch with 0 kg N ha ^–1 or in vetch/rye with 120–130 kg N ha ^–1 than in weeds with 0 and 60 kg N ha ^–1 but at 10–30 cm, it was greater in rye with 120–130 kg N ha ^–1 than in weeds with or without rate. In ST, soil organic C at 0–10 cm was greater in rye with 120–130 kg N ha ^–1 than in rye, vetch, vetch/rye and weeds with 0 and 60 kg N ha ^–1. Soil organic C at 0–10 and 10–30 cm was also greater in NT and ST than in CT. Since 5 to 24% of C accumulation in lint and grain were harvested, C sequestered in cotton and sorghum stalks and roots can be significant in the terrestrial ecosystem and can significantly increase C storage in the soil if these residues are left after lint or grain harvest, thereby helping to mitigate the effects of global warming. Conservation tillage, such as ST, with hairy vetch/rye mixture cover crops and 60–65 kg N ha ^–1 can sustain C accumulation in cotton lint and sorghum grain and increase C storage in the surface soil due to increased C input from crop residues and their reduced incorporation into the soil compared with conventional tillage, such as CT, with no cover crop and N fertilization, thereby maintaining crop yields, improving soil quality, and reducing erosion.     

Relationships ofAmaranthus caudatus

Three species ofAmaranthusare cultivated for their edible seeds:A. hypochondriacus L.,A. cruentusL., andA. caudatusL. The first two are native to Mexico and Guatemala, while the third originated in the Andes. Some authors recognize a fourth species,A. MantegazzianusPass. (A. edulisSpeg.), also from South America. Recent interest in amaranths as crops for improving Third World nutrition makes studies of relationships among amaranth species and intraspecific variation important. The weedy speciesA. hybridus L. (A. quitensisHBK) has been suggested as the progenitor ofA. caudatus, and it appears to be the closest wild relative of the crop. However, discovery of semidomesticated, darkseeded amaranths in Ecuador that are referable toA. caudatusraises some questions. The dark-seeded plants might represent a transitional form between the crop and its weedy progenitor, the product of independent selection of special forms ofA. hybridus, the result of introgressive hybridization between the crop and related weed, established escapes from cultivation, or remnants of the ancestor of the crop which may have been simply wildA. caudatusand notA. hybridus. Detailed morphological comparisons have been made among cultivated forms ofA. caudatus, the semidomesticate, andA. hybridus. Genetic data have been considered, and 2 mixed populations includingA. hybridusand the semidomesticate have been examined. Although all the other hypotheses cannot be eliminated, the dark-seededA. caudatusplants seem most likely to represent escapes from cultivation. Separate recognition ofA. Mantegazzianusdoes not seem warranted.     

Long-term integrated soil fertility management in South-western Nigeria: Crop performance and impact on the soil fertility status

Crop response, tree biomass production and changes in soil fertility characteristics were monitored in a long-term (1986–2002) alley-cropping trial in Ibadan, Nigeria. The systems included two alley cropping systems with Leucaena leucocephala and Senna siamea on the one hand and a control (no-trees) system on the other hand, all cropped annually with a maize–cowpea rotation. All systems had a plus and minus fertilizer treatment. Over the years, the annual biomass return through tree prunings declined steadily, but more drastically for Leucaena than for Senna. In 2002, the nitrogen contribution from Leucaena residues stabilized at about 200 kg N/ha/year, while the corresponding value for Senna was about 160 kg N/ha/year. On average, the four Leucaena prunings were more equal in biomass as well as in amounts of N, P and cations, while the first Sennapruning was always contributing up to 60% of the annual biomass or nutrient return. Maize crop yields declined steadily in all treatments, but the least so in the Senna + fertilizer treatment where in 2002 still 2.2 tonnes/ha of maize were obtained. Nitrogen fertilizer use efficiency was usually higher in the Senna treatment compared to the control or the Leucaena treatment. Added benefits due to the combined use of fertilizer N and organic matter additions were observed only for the Sennatreatment and only in the last 6 years. At all other times, they remained absent or were even negative in the Leucaenatreatments for the first 3 years. Most chemical soil fertility parameters decreased in all the treatments, but less so in the alley cropping systems. The presence of trees had a positive effect on remaining carbon stocks, while they were reduced compared to the 1986 data. Trees had a positive effect on the maintenance of exchangeable cations in the top soil. Exchangeable Ca, Mg and K – and hence ECEC – were only slightly reduced after 16 years of cropping in the tree-based systems, and even increased in the Senna treatments. In the control treatments, values for all these parameters reduced to 50% or less of the original values after 16 years. All the above points to the Senna-based alley system with fertilizers as the more resilient one. This is reflected in all soil fertility parameters, in added benefits due to the combined use of fertilizer nitrogen and organic residue application and in a more stable maize yield over the years, averaging 2.8 tonnes/ha with maximal deviations from the average not exceeding 21%.     

Evolution and improvement of cultivated amaranths

Summary This group of amaranths was studied using four domesticated species (A. hypochondriacus, A. cruentus, A. caudatus, A. caudatus var. atropurpureus and A. edulis), two ancestral weedy species (A. hybridus, A. powellii) and eight hybrids, namely A. edulis A. hypochondriacus, A. edulis X A. caudatus, A. edulis X A. caudatus var. atropurpureus, A. caudatus X A. hybridus, A. edulis X A. hybridus, A. caudatus X A. hypochondriacus, A. hybridus X A. hypochondriacus and A. powellii X A. hypochondriacus.The parents have perfectly normal meiosis and pollen and seed fertility. Except for A. powellii and A. cruentus (n = 17), the species have n = 16. However, the hybrids may be divided into three groups. The first group contains A. edulis X A. cruentus, involving parents with n = 16 and 17, which failed totally, although, under the same conditions, crosses between A. powellii (x = 17) and A hypochondriacus (n = 16) and those between species with n = 16 succeeded with ease. The second group is made up of A. edulis X A. hypochondriacus, A. caudatus X A. hypochondriacus, A. caudatus X A. hybridus, A. edulis X A. hybridus and probably also A. powellii X A. hypochondriacus. Of these, the two combinations, A. caudatus X A. hybridus and A. edulis X A. hybridus, did not proceed beyond the two-leaf stage. At pachytene, the other hybrids showed unmistakable evidence of structural hybridity, with deletions, long or short differentiated segments and inversions. Although bivalents were formed, they possessed a chiasma frequency lower than that of either parent. There was total pollen and seed sterility.The third group comprises A. edulis X A. caudatus, A. edulis X A. caudatus var. atropurpureus and A. hybridus X A. hypochondriacus, which did not show serious developmental defects, the F₁ being vigorous, with good meiotic pairing associated with a reasonable amount of differentiation in the chromosomes leading to 25– 55% fertile pollen and 49 to 66% threshable seed. In the F₂ there were 11–18% unthrifty plants, which disturb the ratios of gene combinations controlling the different characters in the two parents. Plants very near one or both parental phenotypes were recovered, and also those showing different degrees of recombination of characters. Amphidiploids from the F₁ hybrids showed the typical autoploid or segmental alloploid type of meiosis indicating that the parental chromosomes are quite homologous.In view of the present experimental evidence and possible parallel mutations in different grains and weed amaranths, it is not certain whether the cases of natural hybridization and, in particular, of introgression can be taken as evidence for or against the two hypotheses proposed by Sauer (1967) on the basis of his brilliant ecogeographical, morphological, ethnobotanical and archaeological studies of this group of amaranths.The only point that can be stated categorically is that A. caudatus has given rise to A. edulis. The dominance of the characters of A. caudatus over those of A. edulis strengthens such a view, but the latter is sufficiently differentiated morphologically and genetically to deserve independent status. A. caudatus var. atropurpureus is a fertile but unstabilized hybrid segregate between A. caudatus and A. edulis. This is borne out by its morphological, cytogenetic and breeding behaviour, and its hybrids with A. edulis, and, above all, by the recovery of plants identical with this variety from the F₂ progeny of A. edulis X A. caudatus.Whatever the origin of grain types, at present they exist only in cultivation and appear to have a long history, having been selected for large plant body, huge compound inflorescences, large number of female flowers per glomerule, small and soft bracts and pale coloured seed in a dehiscent utricle. At the same time, there has also been inadvertent selection for higher and correctly balanced amounts of protein, carbohydrate and fat.     

Prediction of evapotranspiration and grain yield of rice (Oryza sativa L. cv Thriveni) in a humid tropical climate

Summary In a humid tropical climate at Pattambi (10° 48 N, 76° 12 E), the evapotranspiration (ET) rates of rice (Oryza sativa L. cv. Thriveni) were 2.8–5.7 mm/day during the first crop season (May–September) and 6.2–9.1 mm/day during the second crop season (September–January). The crop was grown at the Station in the irrigated lowlands on sandy soils with average yields of 3025 and 2925 kg/ha in the first and second cropping seasons, respectively. The seasonal ET, water requirements, water use efficiency and field water use efficiency of the crop were 400 mm, 1150 mm, 7.56 and 2.63 kg/ha per mm in the first crop season and 650 mm, 1500 mm, 4.50 and 1.95 kg/ha per millimetre in the second crop season. Using the reference crop ET computed by Blaney-Criddle, Radiation, and Penman methods and measured evaporation from class A pan, Colorado and GGI 3000 pans, the crop coefficients were worked out. Correlations between weather parameters and the biomass of rice were obtained. The grain yield (Y, in kg/ha) of the crop was predicted using the equationY=1.71Y ₀–56S+85F–2430 (N=8,r=0.920), whereY ₀ is the sample of biomass of the rice at flowering in kg/ha,S andF are the duration of sunshine hours and maximum air temperatures (°C) between the 46th day of transplanting and maturity.     

Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice

Background  

Weedy rice (red rice), a conspecific weed of cultivated rice (Oryza sativa L.), is a significant problem throughout the world and an emerging threat in regions where it was previously absent. Despite belonging to the same species complex as domesticated rice and its wild relatives, the evolutionary origins of weedy rice remain unclear. We use genome-wide patterns of single nucleotide polymorphism (SNP) variation in a broad geographic sample of weedy, domesticated, and wild Oryza samples to infer the origin and demographic processes influencing U.S. weedy rice evolution.     

Cultivated and weedy rice interactions and the domestication process

Examining the targets of selection in crop species and their wild and weedy relatives sheds light on the evolutionary processes underlying differentiation of cultivars from progenitor lineages. On one hand, human‐mediated directional selection in crops favours traits associated with the streamlining of controllable and predictable monoculture practices alongside selection for desired trait values. On the other hand, natural selection in wild and especially weedy relatives presumably favours trait values that increase the probability of escaping eradication. Gene flow between crops and wild species may also counter human‐mediated selection, promoting the evolution and persistence of weedy forms. In this issue, two studies from a group of collaborators examine diversity and divergence patterns of genes underlying two traits associated with red rice (Oryza sp.), the conspecific relative of cultivated rice (Oryza sativa) that is a non‐native weed (see Fig. 1 ). In the first study by Gross et al. (2010) , genetic variation in the major gene underlying the hallmark red pigmentation characterizing most weedy rice (Rc) is found to have a pattern consistent with non‐reversion from U.S. cultivated rice (i.e. the cultivar did not ‘go feral’). This suggests that U.S. weedy rice is not an escaped lineage derived from U.S. cultivated rice populations; weedy rice likely differentiated prior to the selective sweep occurred in this gene within cultivated rice populations. Using the major seed shattering locus sh4 gene and the neighbouring genomic region, Thurber et al. (2010) track the molecular evolutionary history of the high shattering phenotype, a trait contributing dramatically to the success of crop selection in cultivated rice as well as the persistence and expansion of weedy red rice. In this study, the shared fixation of a sh4 mutation in both cultivated rice and weedy rice indicates that weedy rice arose subsequent to the strong selective sweep leading to significant reduction in seed shattering in cultivated rice.

Figure 1 Open in figure viewer PowerPoint A weedy, brown hulled red rice individual with long awns surrounded by a field of cultivated rice (photo by A. Lawton‐Rauh).     

Field evaluation of N2-fixation and N-utilization by phaseolus bean varieties determined by15N isotope dilution*

Summary Differences in N₂-fixation byPhaseolus vulgaris bean cultivars were successfully evaluated in the field using¹⁵N isotope dilution technique with a non-fixing test crop of a different species (wheat). The Phaseolus cultivars could have been similarly ranked for N₂-fixation capacity from either seed yield or total nitrogen yield, but the isotope method provided a direct measure of N₂-fixation and made it possible to estimate the proportion of fixed to total nitrogen in the crop and in plant parts. Amounts of nitrogen fixed varied between 24.59 kg N/ha for the 60-day cultivar Goiano precoce to 64.91 kg N/ha for the 90-day cultivar Carioca. The per cent of plant nitrogen due to fixation was 57–68% for the 90-day cultivars and 37% for Goiano precoce (60-day cultivar). Fertilizer utilization was 17–30% of a 20 kg N/ha fertilizer application. 100 kg N/ha fertilizer application decreased N₂-fixation without suppressing it totally. Differences in yield between the highest yielding (Carioca) and the lowest (Moruna) 90-day cultivars were also due apparently to varietal differences in efficiency of conversion of nitrogen to economic matteri.e. seed, as well as to differences in capacity of genotypes for N₂-fixation. The work described here was in part supported by IAEA Research Contract No. RC/2084 UNDP/IAEA Project BRA/78/006     

More than one way to evolve a weed: parallel evolution of US weedy rice through independent genetic mechanisms

Many different crop species were selected for a common suite of ‘domestication traits’, which facilitates their use for studies of parallel evolution. Within domesticated rice (Oryza sativa), there has also been independent evolution of weedy strains from different cultivated varieties. This makes it possible to examine the genetic basis of parallel weed evolution and the extent to which this process occurs through shared genetic mechanisms. We performed comparative QTL mapping of weediness traits using two recombinant inbred line populations derived from crosses between an indica crop variety and representatives of each of the two independently evolved weed strains found in US rice fields, strawhull (S) and blackhull awned (B). Genotyping‐by‐sequencing provided dense marker coverage for linkage map construction (average marker interval <0.25 cM), with 6016 and 13 730 SNPs mapped in F₅ lines of the S and B populations, respectively. For some weediness traits (awn length, hull pigmentation and pericarp pigmentation), QTL mapping and sequencing of underlying candidate genes confirmed that trait variation was largely attributable to individual loci. However, for more complex quantitative traits (including heading date, panicle length and seed shattering), we found multiple QTL, with little evidence of shared genetic bases between the S and B populations or across previous studies of weedy rice. Candidate gene sequencing revealed causal genetic bases for 8 of 27 total mapped QTL. Together these findings suggest that despite the genetic bottleneck that occurred during rice domestication, there is ample genetic variation in this crop to allow agricultural weed evolution through multiple genetic mechanisms.     

Persistence of sunflower crop traits and fitness in Helianthus petiolaris populations

Transgenic plants have increased interest in the study of crop gene introgression in wild populations. Genes (or transgenes) conferring adaptive advantages persist in introgressed populations, enhancing competitiveness of wild or weedy plants. This represents an ecological risk that could increase problems of weed control. Introgression of cultivar alleles into wild plant populations via crop–wild hybridisations is primarily governed by their fitness effect. To evaluate this, we studied the second generation of seven wild–crop interspecific hybrids between weedy Helianthus petiolaris and cultivated sunflower, H. annuus var. macrocarpus. The second generation comprised open‐pollinated progeny and backcrosses to the wild parent, mimicking crosses that occur in natural situations. We compared a number of morphological, life history and fitness traits. Multivariate analysis showed that the parental species H. annuus and H. petiolaris differed in a number of morphological traits, while the second hybrid generation between them was intermediate. Sunflower crop introgression lowered fitness of interspecific hybrids, but fitness parameters tended to recover in the following generation. Relative frequency of wild/weedy and introgressed plants was estimated through four generations, based on male and female parent fitness. In spite of several negative selection coefficients observed in the second generation, introgressed plants could be detected in stands of <100 weedy H. petiolaris populations. The rapid recovery of fecundity parameters leads to prediction that any trait conferring an ecological advantage will diffuse into the wild or weedy population, even if F1 hybrids have low fitness.