Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity
Wei HuChangmian JiZhe LiangJianqiu YeWenjun OuZehong DingGang ZhouWeiwei TieYan YanJinghao YangLiming MaXiaoying YangYunxie WeiZhiqiang JinJianghui XieMing PengWenquan WangAnping GuoBiyu XuJianchun GuoSongbi ChenMingcheng WangYang ZhouXiaolong LiRuoxi LiXinhui XiaoZhongqing WanFeifei AnJie ZhangQingyun LengYin LiHaitao ShiRay MingKaimian Li
23
Citation
76
Reference
10
Related Paper
Citation Trend
Abstract:
Abstract Background Heterozygous genomes are widespread in outcrossing and clonally propagated crops. However, the variation in heterozygosity underlying key agronomic traits and crop domestication remains largely unknown. Cassava is a staple crop in Africa and other tropical regions and has a highly heterozygous genome. Results We describe a genomic variation map from 388 resequenced genomes of cassava cultivars and wild accessions. We identify 52 loci for 23 agronomic traits through a genome-wide association study. Eighteen allelic variations in heterozygosity for nine candidate genes are significantly associated with seven key agronomic traits. We detect 81 selective sweeps with decreasing heterozygosity and nucleotide diversity, harboring 548 genes, which are enriched in multiple biological processes including growth, development, hormone metabolisms and responses, and immune-related processes. Artificial selection for decreased heterozygosity has contributed to the domestication of the large starchy storage root of cassava. Selection for homozygous GG allele in MeTIR1 during domestication contributes to increased starch content. Selection of homozygous AA allele in MeAHL17 is associated with increased storage root weight and cassava bacterial blight (CBB) susceptibility. We have verified the positive roles of MeTIR1 in increasing starch content and MeAHL17 in resistance to CBB by transient overexpression and silencing analysis. The allelic combinations in MeTIR1 and MeAHL17 may result in high starch content and resistance to CBB. Conclusions This study provides insights into allelic variation in heterozygosity associated with key agronomic traits and cassava domestication. It also offers valuable resources for the improvement of cassava and other highly heterozygous crops.Keywords:
Outcrossing
Balancing selection
In this paper, different definitions of animal domestication are examined. Methods for identifying the domestication processes are outlined, including zooarchaeological and biomolecular techniques, along with archaeological evidence of associated economic and social changes. The extent to which animal domestications can be seen as hunter-gatherer innovations rather than a later addition by plant agriculturalists is discussed. The undisputed hunter-gatherer innovation of dog domestication is taken as a case study, and horse domestication in central Asia is also considered in depth. Other possible examples of domestication of animals by hunter-gatherers either before, or synchronously with, plant domestication are highlighted, including cattle in North Africa, camelids in South America, and reindeer in northern Eurasia. The reasons why animal domestication usually post-dates plant domestication are explored.
Cite
Citations (2)
AN ANALYSIS OF OUTCROSSING IN CERTAIN COMPLEX‐HETEROZYGOUS EUOENOTHERAS. I. FREQUENCY OF OUTCROSSING
H off , V ictor J. (U. Arkansas, Fayetteville.) An analysis of outcrossing in certain complex‐heterozygous Euoenotheras. I. Frequency of outcrossing. Amer. Jour. Bot. 49(7): 715–721. 1962.—Eleven complex‐heterozygous races of Euoenothera were used for study. The races were grown in the midst of the experimental garden in which plants from approximately 150 races and hybrid combinations were growing together in close proximity so as to afford the maximum opportunity for outcrossing. Many capsules (126) resulting from unguarded flowers were collected from the chosen races and the seed grown to determine the number of hybrid plants resulting from outcrossing within each fruit. Among the various capsules, the number of outcrosses ranged from 0% to over 50% of the plants grown, while the total amount of outcrossing ranged from 0.7 to 7.8% among 5 different collections of capsules. A relationship between the amount of pollen produced by a flower or normally deposited on its stigma and the degree of outcrossing was noted. It is concluded that outcrossing probably occurs with sufficient frequency to account for the large number of complex‐combinations found in nature.
Outcrossing
Outbreeding depression
Cite
Citations (19)
Phenotypic trait
Cite
Citations (292)
Abstract Diversity levels in populations of barley landraces may be influenced by varying levels of natural outcrossing caused by environmental conditions. Outcrossing was studied in 10 accessions of the barley landrace Arabi Aswad from different environments in Syria. Electrophoretic variation at two codominant isoenzymes ( Est1 and Est2 ) in six seeds of 50 families per population were analysed and multilocus outcrossing rates calculated. Results were correlated with interpolated environmental conditions. Outcrossing was, on average, 1.7% and not significantly different from the outcrossing rate of wild barley. A significant increase of outcrossing was observed with increasing inter‐annual variation in rainfall and decreasing minimum temperatures of the coldest month.
Outcrossing
Natural population growth
Cite
Citations (20)
Seed production is the limiting factor for hybrid rice expansion. The hybrid parents' outcrossing ability is the key point to increase seed production. To breed for outcrossing ability, it is necessary to dispose of variability and evaluate, as soon as possible (S 1, S2), this character. Estimation of female outcrossing ability is possible for lines segregating for a recessive male-sterile gene. The grain yield of male-sterile plants, outcrossed by fertile plants, either of the same line or by fertile plants of another line, is an estimation of outcrossing ability. Using this first method, we evaluated the outcrossing ability of 62 S2 lines coming from a cross between two inbred lines (one msms). With the second method, we evaluated outcrossing ability of 130 S1 lines extracted from a recurrent population segregating ms gene. The 130 lines were outcrossed by four testers: three inbred lines and a population. Significant differences were observed among S2lines (outcrossing ability ranged from 2% to 54%). A good correlation was observed between outcrossing by each tester. For both trials, an important variability was observed. Selection for female outcrossing aptitude is thus possible and important genetic progresses are to be hoped. Outcrossing ability evaluation of future B lines, at S1 and S2 stages, is now integrated into all breeding programs that CIRAD and its partners lead in Latin America. This outcrossing ability evaluation method can be used for phenotyping lines, allowing molecular breeding to speed up creation strong of A and B lines with strong outcrossing ability. (Resume d'auteur)
Outcrossing
Cite
Citations (0)
Outcrossing rate is an important determinant of cytoplasmic male sterile (CMS) breeding and hybrid seed production for heterosis in soybean. Parental lines with a high outcrossing rate were screened for backcross breeding to obtain the high outcrossing rate maintenance B-lines and sterile A-lines. Application in production practices will help to increase hybrid soybean production. In this study, JLCMS82B and JLCMS89B were selected as parents for the construction of outcrossing rate segregation populations, and the progeny-array approach (PAA) and glyphosate resistant gene markers were used to determine outcrossing rates. We found that: (1) The outcrossing rate between JLCMS82B and JLCMS89B was significantly different; (2) the outcrossing rate of the F2 segregating populations was a quantitative trait, though whether an additive or epistatic effect exists required analysis with a triple test intersection analysis; (3) agronomic traits correlated with outcrossing rate; outcrossing rate was the highest with plant height of about 84 cm, lower number of plant branches, earlier flowering time, larger angle between the branches and the main stem, and with more divergent plant morphology. Correlation analysis between agronomic traits and outcrossing rate can effectively guide the screening of parents with a high outcrossing rate.
Outcrossing
Epistasis
Outbreeding depression
Genetic architecture
Trait
Cite
Citations (4)
This chapter discusses how societal demands can affect the domestication process and how this affects domestic animals compared with their wild counterparts. The different conceptions of domestication, domestication from a modern ethological point of view will, the animals' perception of humans and changes in the way that animal domestication processes are considered are also included.
Affect
Cite
Citations (2)
The far Southwest Ethiopians transplant wild plant species to their gardens. One of such plant is the Dioscorea that we studied to assess the knowledge of wild yam and process of domestication. The study links two types of evidence to obtain insight about the process of yam domestication. We analyze two data sets derived from (1) ethnobotanical survey using 231 semi-structured interviews; and (2) morphological study in 47 yam accessions. Our study revealed that domestication is still active in some villages. Knowledge of yam domestication was shared by 44% of the farmers' even by those that have never practiced its domestication. Farmers who can describe the trend of domestication and the morphotypes of domesticate represented 21 and 28%, respectively. Farmers who have recent transplants in their garden varied from 4% in Bench to 10% in Sheko. The domestication process described by the two ethnic groups is similar. The duration of domestication can take up to six years, but with most of the individuals, it only takes three to five years. By linking the two types of evidence, two evolutionary processes are distinguished: (1) populations of recent domesticate expressing a domestication syndrome possibly belongs to the wild D. abyssinica or D. praehensilis, and (2) plants of incipient domesticate that might be derived from volunteers or diverse types of hybrids. Each of these processes can lead to integration of wild genotypes into the cultivated gene pool, and hence, enhance genetic diversity of cultivated yams. The domestication practices of traditional farmers should thus be taken into account if yam conservation and improvement plans need to be established.
Ethnobotany
Cite
Citations (3)
The pig appears to have been among the earliest domesticated animals in China, with evidence for pig domestication at Cishan from 8000 BP. The authors propose a model for the development of animal domestication.
Cite
Citations (135)
An Analysis of Outcrossing in Certain Complex-Heterozygous Euoenotheras. I. Frequency of Outcrossing
Hoff, Victor J. (U. Arkansas, Fayetteville.) An analysis of outcrossing in certain complex-heterozygous Euoenotheras. I. Frequency of outcrossing. Amer. Jour. Bot. 49(7): 715–721. 1962.—Eleven complex-heterozygous races of Euoenothera were used for study. The races were grown in the midst of the experimental garden in which plants from approximately 150 races and hybrid combinations were growing together in close proximity so as to afford the maximum opportunity for outcrossing. Many capsules (126) resulting from unguarded flowers were collected from the chosen races and the seed grown to determine the number of hybrid plants resulting from outcrossing within each fruit. Among the various capsules, the number of outcrosses ranged from 0% to over 50% of the plants grown, while the total amount of outcrossing ranged from 0.7 to 7.8% among 5 different collections of capsules. A relationship between the amount of pollen produced by a flower or normally deposited on its stigma and the degree of outcrossing was noted. It is concluded that outcrossing probably occurs with sufficient frequency to account for the large number of complex-combinations found in nature.
Outcrossing
Cite
Citations (9)