Cacao domestication II: progenitor germplasm of the Trinitario cacao cultivar

Cacao (Theobroma cacao L.) has been cultivated in Central America since pre-Columbian times. The type of cacao cultivated in this region was called Criollo; cacao populations from the Amazon basin were called Forastero. The type of Forastero most commonly cultivated until 1950 was named Amelonado. Historical data show Trinitario cacao to have originated in Trinidad, resulting from natural hybridisation between Criollo and Amelonado Forastero. Doubts persist on the source of the Amelonado Forastero involved in the origin of Trinitario; the Amelonado parent may have come from the Lower Amazon, the Orinoco or the Guyanas. Most of the cacao cultivated worldwide until 1950 consisted of Criollo, Trinitario and Amelonado. From the early 1950s, Forastero material collected in the Upper Amazon region during the 1930s and 1940s began to be employed in breeding programmes. To gain a better understanding of the origin and the genetic basis of the cacao cultivars exploited before the utilisation of germplasm collected in the Upper Amazon, a study was carried out using restriction fragment length polymorphism and microsatellite markers. Trinitario samples from 17 countries were analysed. With molecular markers, it was possible to clearly identify three main genotypes (represented by clones SP1, MAT1-6 and SIAL70) implicated in the origin of most Trinitario clones.     

SNP deserts of Asian cultivated rice: genomic regions under domestication

When performing a genome‐wide comparison between indica (93‐11) and japonica (Nipponbare), we find 8% of the genome, which have an extremely low SNP rate (< 1 SNP/kb). Inside these ‘SNP deserts’, experimentally confirmed genes show increased K_a/K_s that indicate adaptive selection. To further elucidate this connection, we survey the level and pattern of genetic variation in both cultivated and wild rice groups, using 155 noncoding regions located within SNP deserts. The results suggest that cultivated rice has greatly reduced genetic variation within SNP deserts as compared to either the nondesert or corresponding genomic regions in wild rice. Consistent with this reduction in genetic variation, we find a biased distribution of derived allele frequency in the cultivated group, indicative of positive selection. Furthermore, over half of the confirmed, domestication‐related genes are found within SNP deserts, also suggesting that SNP deserts are strongly related to domestication, and might be the key sites in the process of domestication.     

Translocation of phosphorus-32 into wilting and healthy fruits of cacao (Theobroma Cacao)

Summary The uptake of phosphorus into young cacao fruits (cherelles) was studied by applying 1.0 mC of P-32 to tins of soil in which young cacao trees were growing. The radiation from the fruits was measured daily with a shielded end-window G-M tube until the fruit wilted. While the fruit remained healthy accumulation of P-32 was linear and uptake continued for about three days after the fruit stopped growing (the first sign of wilting); uptake of P-32 then ceased. An increase in the count rate as the fruit became flaccid was attributed to reduced self-absorption due to loss of water.The distribution of the radio-active phosphorus in the seeds and pericarp was investigated and comparative analyses of phosphate in wilting and healthy fruits are presented.The results provide additional evidence for the hypothesis that cherelle wilt is analogous to a fruit-thinning mechanism.     

The Growth of Cacao (Theobroma cacao) With and Without Shade: With one Figure in the Text

Evidence is presented that young plants of cacao can toleratehigh light intensities if provided with adequate water and nutrientsupplies.     

The origin of the cultivated tomato

The ancestral form of the cultivated tomato was originally confined to the Peru-Ecuador area. After spreading north possibly as a weed in pre-Columbian times it was not extensively domesticated until it reached Mexico, and from there the cultivated forms were disseminated.     

Xylem Occlusions in the Fruit of Cacao (Theobroma cacao) and their Relation to Cherelle Wilt

The anatomy and distribution of the xylem of the fruit of cao(Theobroma cacao) has been investigated by injection and stainingtechniques. The physical symptoms of cherelle wilt (pod wilt), a physiologicalfruitthinning mechanism, have been shown to be caused by occlusionsin the xylem vessels of the fruit-stalk. The initiation of theseocclusions in thought to be associated with the oxidative activityof a cambial or meristermatic band of tissue, which forms newvascular tissue to the pericarp.     

On the origin of cultivated rye

The origin of cultivated rye has been studied, taking into consideration evidence from various fields. Based on morphological resemblances and cytogenetic affinities, cultivated rye is included in Secale cereale L. emend. Sencer, which also includes annual wild and weedy ryes. Wild populations of 5. cereale , which have evolved from Secale montanum Guss. emend. Sencer, invaded wheat and barley fields during the early days of cultivation and gave rise to weedy ryes with varying degrees of rachis brittleness. Cultivated rye was selected from weedy ryes for non-brittle rachis and bigger caryopsis both unconsciously and consciously by man. The geographic origin of cultivated rye is postulated for the Büyük Ari Dai (Mt. Ararat) and Lake Van area in eastern Turkey. It spread from this area as a weed in wheat and barley fields towards the north, east and west and imposed itself as a secondary crop under conditions unfavourable for wheat and barley. It thus became a crop in its own right in several places independently, in addition to it being known by the people living in the Caucasus and Transcaucasus from very early agricultural times.     

Genetic Diversity and Natural Population Structure of Cacao (Theobroma cacao L.) from the Brazilian Amazon Evaluated by Microsatellite Markers

A sample of 94 accessions of Theobroma cacao L. (cacao), representing four populations from the Brazilian Amazon (Acre, Rondônia, lower Amazon and upper Amazon) were analyzed using microsatellite markers to assess the genetic diversity and the natural population structure. From the 19 microsatellite loci tested, 11 amplified scorable products, revealing a total of 49 alleles, including two monomorphic loci. The Brazilian upper Amazon population contained the largest genetic diversity, with the most polymorphic loci, the highest observed heterozygosity; and the majority of rare alleles, thereby this region might be considered part of the center of diversity of the species. The observed heterozygosity for all the Brazilian populations (H _o = 0.347) was comparable with values reported for other similar upper Amazon Forastero cacao populations, with the Acre and Rondônia displaying the lowest values. The lower Amazon population, traditionally defined as highly homozygous, presented an unexpectedly high observed heterozygosity (H _o = 0.372), disclosing rare and distinct alleles, with large identity with the upper Amazon population. It was hypothesized that part of the lower Amazon population might derive from successive natural or intentional introduction of planting material from other provenances, mainly upper Amazon. Most of the loci exhibited a lower observed heterozygosity than expected, suggesting that self-pollination might be more common than usually assumed in cacao, but excess of homozygotes might also derive from sub-grouping (Wahlund effect) or from sampling related individuals. Most of the gene diversity was found to occur within groups, with small differentiation between the four Brazilian Amazon populations, typical of species with high gene flow.     

The origin of the domestic pig: independent domestication and subsequent introgression

The domestic pig originates from the Eurasian wild boar (Sus scrofa). We have sequenced mitochondrial DNA and nuclear genes from wild and domestic pigs from Asia and Europe. Clear evidence was obtained for domestication to have occurred independently from wild boar subspecies in Europe and Asia. The time since divergence of the ancestral forms was estimated at approximately 500,000 years, well before domestication approximately 9,000 years ago. Historical records indicate that Asian pigs were introduced into Europe during the 18th and early 19th centuries. We found molecular evidence for this introgression and the data indicated a hybrid origin of some major "European" pig breeds. The study is an advance in pig genetics and has important implications for the maintenance and utilization of genetic diversity in this livestock species.     

Implications of domestication and rearing conditions for the behaviour of cultivated fishes

Farmed fishes are often selectively bred for desirable production traits, such as rapid growth, that brings with them behavioural differences. In addition, the striking differences in the environment experienced by wild and cultured fishes offers considerable scope both for unplanned, natural selection for different inherited behavioural phenotypes and for behavioural differences arising from differential experience. In this paper, the evidence that such processes have produced behavioural differences between wild and cultured fishes is reviewed in relation to feeding, antipredator responses, aggression and reproductive behaviour. The reported findings are discussed in relation to the concept of 'behavioural syndromes', or suites of co‐varying behavioural traits that adapt individuals of the same population to spatial and temporal variation in selection regimes. The implications of the behaviour of cultured fishes for their welfare in production cages, for the environmental impact of escapees on wild stocks and for the success of hatchery‐based restocking programmes are considered. The review inevitably concentrates on salmonids, in which such phenomena have been intensively researched.     

A Composite Linkage Map from Three Crosses Between Commercial Clones of Cacao, Theobroma cacao L.

In this paper, we report the construction of the first composite map of cacao from linkage data of one F₂ and two F₁ mapping populations with a high number of codominant markers in common. The combination of linkage information from all three maps results in the currently most precise estimates of marker locations and distances between markers, especially in densely marked areas. JoinMap®V4 software was used for all marker quality assessment and mapping. Individual (sub-composite) maps and the composite map contained 10 major linkage groups, corresponding to the number of cacao chromosomes. Homogeneity of marker placement was very high among sub-composite maps, the composite map, and the designated “reference” map. Care was exercised in the re-creation of sub-composite maps and the composite map to include only markers with acceptable mapping quality parameters. The composite map places more markers with higher precision than any individual map. This research clearly demonstrates for the first time a very high level of marker homogeneity among commercial cacao clones compared to other species. The observed homogeneity between different maps, including the composite one, is probably due to a narrow genetic base of commercial cacao clones. Markers linked to identified quantitative trait loci (QTLs) are more likely to retain linkage in other commercial clones, rendering the QTLs in cacao potentially more stable than in other species.     

家养动物驯化起源的研究方法与进展

驯化动物伴随了人类上万年的进化历程。在驯化过程中, 家养动物表型和行为特征发生巨大改变, 并与人类生产生活的进步相适应。研究动物驯化问题对于了解遗传多样性及适应性进化, 解析复杂性状的遗传机制等具有重要的意义, 成为生物学领域的重点研究内容之一。本文专注于动物驯化的初始阶段, 首先介绍了驯化起源的时间与地点、驯化途径和驱动因、驯化后的扩散和品种选育; 其次从驯化对象的角度着重介绍了考古学、分子和群体遗传学两方面的家养动物驯化起源的研究策略、优势与不足, 以及未来的发展方向; 最后, 我们综合多方面的证据, 介绍了在中国驯化的家猪(Sus domesticus)和家鸡(Gallus gallus domesticus)以及其他主要家养动物考古和分子水平上驯化起源的研究进展。本文整合多种证据为家养动物驯化起源的研究提供了相对完整的视角和新的思路。     

Studies of Fruit Development of Cacao (Theobroma cacao) in Relation to Cherelle wilt: III. Effects of fruit-thinning

Cacao trees were manually thinned to 1, 2, or 10 pods per treein order to observe the effect of competition onwilting behaviour.The number of pods wilting and harvested were recorded weeklyfor I6 months. The percentage of pods that wilted on the thinnedtrees was less than the controls. However, yields were reducedon the thinned trees more than expected owing to the continuedwilting of those pods left on the trees. The results supportthe hypothesis that cherelle with is a fruit thinning mechanism,but that biotic factors can cause the same syndrome.     

家养动物的起源与驯化研究进展

动物的驯化是新石器时代农业革命的主要内容之一, 导致了人类生活方式从狩猎向畜牧的转变。开展家养动物起源与驯化的研究, 不仅有助于了解人类社会的发展史和人工选择下动物的进化过程, 而且有助于开展家养动物的良种选育和遗传多样性保护, 因此该研究领域受到了人们的长期关注。近年来, 随着更多考古证据的发现与分子遗传学的发展, 人们对于家养动物的起源与驯化有了更深入的认识。本文对家养动物起源与驯化研究中一些基本问题的研究方法和进展进行了综述。文章第一部分介绍了家养动物的野生祖先、起源地、起源时间、建群者大小和扩散路线等问题; 第二部分则涉及家养动物驯化的条件、过程、性状改变及其遗传机制等方面。最后指出了家养动物起源与驯化研究中依然存在的问题, 并对未来研究发展的趋势进行了讨论。     

Dispersion models and sampling of cacao mirid bug Sahlbergella singularis (Hemiptera: Miridae) on Theobroma Cacao in southern Cameroon

The spatio-temporal distribution of Sahlbergella singularis Haglung, a major pest of cacao trees (Theobroma cacao) (Malvaceae), was studied for 2 yr in traditional cacao forest gardens in the humid forest area of southern Cameroon. The first objective was to analyze the dispersion of this insect on cacao trees. The second objective was to develop sampling plans based on fixed levels of precision for estimating S. singularis populations. The following models were used to analyze the data: Taylor's power law, Iwao's patchiness regression, the Nachman model, and the negative binomial distribution. Our results document that Taylor's power law was a better fit for the data than the Iwao and Nachman models. Taylor's b and Iwao's β were both significantly >1, indicating that S. singularis aggregated on specific trees. This result was further supported by the calculated common k of 1.75444. Iwao's α was significantly <0, indicating that the basic distribution component of S. singularis was the individual insect. Comparison of negative binomial (NBD) and Nachman models indicated that the NBD model was appropriate for studying S. singularis distribution. Optimal sample sizes for fixed precision levels of 0.10, 0.15, and 0.25 were estimated with Taylor's regression coefficients. Required sample sizes increased dramatically with increasing levels of precision. This is the first study on S. singularis dispersion in cacao plantations. Sampling plans, presented here, should be a tool for research on population dynamics and pest management decisions of mirid bugs on cacao.