Genomic dissection of widely planted soybean cultivars leads to a new breeding strategy of crops in the post-genomic era

Soybeans specially the widely planted cultivars have been dramatically improved in agronomic performance and is well adapted to local planting environments after long-time domestication and breeding.Uncovering the unique genomic features of popular cultivars will help to understand how soybean genomes have been modified through breeding.We re-sequenced 134 soybean cultivars that were released and most widely planted over the last century in China.Phylogenetic analyses established that these cultivars comprise two geographically distinct sub-populations:Northeast China (NE) versus the HuangHuai-Hai River Valley and South China (HS).A total of 309 selective regions were identified as being impacted by geographical origins.The HS sub-population exhibited higher genetic diversity and linkage disequilibrium decayed more rapidly compared to the NE sub-population.To study the association between phenotypic differences and geographical origins,we recorded the vegetative period under different growing conditions for two years,and found that clustering based on the phenotypic data was closely correlated with cultivar geographical origin.By iteratively calculating accumulated genetic diversity,we established a platform panel of cultivars and have proposed a novel breeding strategy named "Potalaization"for selecting and utilizing the platform cultivars that represent the most genetically diversity and the highest available agronomic performance as the "plateau"for accumulating elite loci and traits,breeding novel widely adapted cultivars,and upgrading breeding technology.In addition to providing new genomic information for the soybean research community,the "Potalaization"strategy that we devised will also be practical for integrating the conventional and molecular breeding programs of crops in the post-genomic era.

THE CULTURE HISTORY AND BREEDING STRATEGY OF POPLAR IN ITALY

INTRODUCTION In Italy,they have done many bcnefi-cial works in the high yield plantation--the culture and the breeding of Poplar.Forexample,in our country,introduced manygood clones such as I—214,I—72 and I—69etc.all the clones were the production of

Strategy for Use of Rice Blast Resistance Genes in Rice Molecular Breeding

Rice blast is one of the most destructive diseases affecting rice production worldwide.The development and rational use of resistant varieties has been the most effective and economical measure to control blast.In this review,we summarized the cloning and utilization of rice blast resistance genes,such as Pi1,Pi2,Pi9,Pi54,Pigm and Piz-t.We concluded that three main problems in the current breeding of rice blast resistance are:availability of few R(resistance)genes that confer resistance to both seedling and panicle blast,the resistance effect of pyramided lines is not the result of a simple accumulation of resistance spectrum,and only a few R genes have been successfully used for molecular breeding.Therefore,novel utilization strategies for rice blast R genes in molecular breeding were proposed,such as accurately understanding the utilization of R genes in main modern rice varieties,creating a core resistant germplasm with excellent comprehensive traits,screening and utilizing broadspectrum and durable resistance gene combinations.Lastly,the trends and possible development direction of blast resistance improvement were also discussed,including new genes regulating resistance identified via GWAS(genome-wide association study)and improving rice blast resistance using genetic editing.

Practices and Prospects of Super Hybrid Rice Breeding

The great progress in super rice breeding both in China and other countries has been made in recent years. However, there were three main problems in super rice breeding： 1） the super rice varieties were still rare; 2） most super rice varieties exhibited narrow adaptability; and 3） current breeding theories emphasized too much on the rice growth model, but they were unpractical in guidance for rice breeding. According to the authors＇ experience on the rice breeding, the breeding strategies including three steps （super parent breeding, super hybrid rice breeding and super hybrid rice seed production） were proposed, and the objectives of each step and the key technologies to achieve the goals were elucidated in detail. The super parent of hybrid rice should exhibit excellent performance in all agronomic traits, with the yield or sink capacity reached the level of the hybrid rice control in regional trials. The super hybrid rice combination should meet the following criteria： good rice quality, wide adaptation, lodging resistance, resistance to main insects and diseases, and the yield exceeded above 8% over the control varieties in the national and provincial regional trials. To achieve the goal, the technical strategies, such as selecting optimal combination of the parents, increasing selection pressure, paying more attention to harmony of ideal plant type, excellent physiological traits and all the agronomic traits, should be emphasized. The yield of seed production should reach 3.75 t/ha and 5.25 t/ha for the super hybrid rice combinations derived from early-season and middle-season types of male sterile lines, respectively. The main technologies for raising seed production yield included selecting optimum seed production site, using the male sterile line with large sink capacity and good outcrossing characteristics, and improving the amount of the pollen by intensive cultivation of the male parent. According to the technologies of the three-step breeding on super hybrid rice, two super rice parents, including a male parent 996 and a thermo（photo）-genic male sterile [T（P）GMS] line C815S, were bred. Furthermore, a super early hybrid rice combination, Luliangyou 996, which could be used as a double-season early rice variety in middle and lower reaches of the Yangtze River, China, was bred by using the super rice varlet3, 996 as the male parent, and several hybrid rice combinations with higher yield than control variety in regional trials both of Hunan Province and state were bred with the T（P）GMS line C815S as the female parent.

Research progress on the breeding of japonica super rice varieties in Jiangsu Province,China

In this study we report the results of a decade-long breeding program for japonica super rice made by Nanjing Branch of Chinese National Center for Rice Improvement in Jiangsu Academy of Agricultural Sciences. We concluded that selection of parents with good comprehensive traits and complementary advantages and disadvantages of both parents in the hybrid combination, and early selection of high heritability traits in earlier segregating generations could significantly improve the breeding efficiency. The use of closely-linked functional markers in pyramiding of multiple genes could greatly increase breeding efficiency, avoiding time-consuming and laborious steps that were used in traditional breeding program. It is also important to coordinate the yield components with variety characteristics such as yield stability, wide adaptability, lodging resistance, and an attractive grain appearance during late growth stage of rice.

Simulation Modeling in Plant Breeding: Principles and Applications

Conventional plant breeding largely depends on phenotypic selection and breeder＇s experience, therefore the breeding efficiency is low and the predictions are inaccurate. Along with the fast development in molecular biology and biotechnology, a large amount of biological data is available for genetic studies of important breeding traits in plants, which in turn allows the conduction of genotypic selection in the breeding process. However, gene information has not been effectively used in crop improvement because of the lack of appropriate tools. The simulation approach can utilize the vast and diverse genetic information, predict the cross performance, and compare different selection methods. Thus, the best performing crosses and effective breeding strategies can be identified. QuLine is a computer tool capable of defining a range, from simple to complex genetic models, and simulating breeding processes for developing final advanced lines. On the basis of the results from simulation experiments, breeders can optimize their breeding methodology and greatly improve the breeding efficiency. In this article, the underlying principles of simulation modeling in crop enhancement is initially introduced, following which several applications of QuLine are summarized, by comparing the different selection strategies, the precision parental selection, using known gene information, and the design approach in breeding. Breeding simulation allows the definition of complicated genetic models consisting of multiple alleles, pleiotropy, epistasis, and genes, by environment interaction, and provides a useful tool for breeders, to efficiently use the wide spectrum of genetic data and information available.

Nest-site selection and breeding ecology of Streaked Wren-Babbler(Napothera brevicaudata)in a tropical limestone forest of southern China

Background: The breeding information of most birds in Asian tropical areas,especially in limestone forests,is still poorly known.The Streaked Wren-Babbler(Napothera brevicaudata) is an uncommon tropical limestone bird with a small range.We studied its nest-site selection and breeding ecology,in order to understand the adaptations of birds to the conditions of tropical limestone forest in southern China.Methods: We used methods of systematical searching and parent-following to locate the nests of the Streaked Wren-Babbler.We measured characteristics of nest sites and rock cavities.Data loggers and video cameras were used to monitor the breeding behavior.Results: All the observed nests of the Streaked Wren-Babbler were placed in natural shallow cavities or deep holes in large boulders or limestone cliffs.The great majority(96.6%) of Streaked Wren-Babbler nests had three eggs with an average fresh weight of 3.46-± 0.43 g(n = 36,range 2.52-4.20 g).Most(80.4%) females laid their first eggs between March and April(n = 46).The average incubation and nestling period of the Streaked Wren-Babbler was 10.2 range 9-11 days),respectively.Most(87.9%) nests h± 0.4 days(n = 5,range 1011 days) and 10.5 ± 0.8 days(n = 6,ad at least one nestling fledge between 2011 and 2013(n = 33).Conclusions: Our study suggests that several features of the breeding ecology of the Streaked Wren-Babbler,including building nests in rocky cavities,commencing breeding earlier than most species,and reducing foraging times during the incubation period,are well-adapted to the unique habitat of tropical limestone forest.

Mechanism of Sterility and Breeding Strategies for Photoperiod/Thermo-Sensitive Genic Male Sterile Rice

To understand the male sterility mechanism of photoperiod/thermo-sensitive genic male sterile [P（T）GMS] lines in rice, the research progress on genetics of photoperiod and/or temperature sensitive genic male sterility in rice was reviewed. A new idea was proposed to explain the sterility mechanism of P（T）GMS rice. The fertility transition from sterile to fertile is the result of cooperative regulation of major-effect sterile genes with photoperiod and/or temperature sensitive genes, but not the so-called pgms gene in P（T）GMS rice. The minor-effect genes, which exhibit accumulative effect on sterility, are the important factors for the critical temperature of sterility transition. The more minor-effect genes the sterile line holds, the lower the critical temperature of sterility transition is. The critical temperature of sterility transition will be invariable if all the minor-effect genes are homozygous. The strategies for breeding P（T）GMS rice were also proposed. The selective indices of critical photoperiod and temperature for sterility transition should be set according to varietal type and ecological region. Imposing selection pressure is a key technology for breeding P（T）GMS rice with lower critical temperature for sterility, and improving the comprehensive performance of the whole traits and combining ability is vital for breeding P（T）GMS rice lines.

Theoretical analyses of testing efficiency in long-term breeding of poplar

The major goal for long-term poplar breeding can be formulated as maximizing annual progress in Group Merit Gain at a given annual budget （GMG/Y＊）. To evaluate different breeding scenarios, a deterministic simulator BREEDING CYCLE ANALYZER covering the most important aspects （gain, cost, time, technique, and gene diversity） of a full breeding cycle was used. The breeding strategies considered was based on pairwise crossing of the selected breeding population and balanced within family selection for the next breeding population. A main scenario and a number of alternative scenarios within these constraints were evaluated using estimates of the best available inputs for poplars. In focus was a comparison between three different testing scenarios for selecting the parents mated to create future breeding generations, thus selecting based on phenotype, clone test or progeny test. For the main scenario, the highest GMG/Y, and the optimal selection age for clone, phenotype and progeny strategies were 0.7480 %, 0.6989% and 0.4675%; 7, 6, and 11 years respectively. Clone test was best except when heritability was high, plant price was high or total budget was low; phenotype strategy was the second except for the case of extremely low narrow-sense heritability, for which the progeny strategy was a little more efficient than phenotype strategy. GMG/Y was markedly affected by narrow-sense heritability, additive variance at mature age, rotation age, plant-dependent cost, total budget and the time needed to produce the test plants, while diversity loss and recombination cost had rather weak effect on GMG/Y. Short rotation age and cheap testing cost favoured all three testing strategies. Comparably short rotation age, low plant-dependent cost and high total budget seem to promote early selection for progeny strategy.

Germplasm resources and genetic improvement of Akebia:A new fruit crop in China

Akebia species,belonging to Lardizabalaceae,are widespread from subtropical to temperate environments of China,Japan,and Korea.All known Akebia species have medicinal and dietary value and have been widely cultivated as a new fruit crop in many areas of China.However,compared with other crop species,the breeding improvement and commercial cultivation of Akebia remain in their infancy.This review systematically introduces the present germplasm resources,geographical distribution,biological characteristics,interspecific and intraspecific cross compatibility,molecular biology,and breeding progress in Akebia species.Akebia plants are widely distributed in Shanxi,Henan,Sichuan,Chongqing,Hunan,Hubei,Jiangxi,Zhejiang,and Fujian provinces of China,and wild Akebia plants exhibit abundant phenotypic and genetic diversity due to their wide range of geographical distribution and high adaptability in different habitats.Interspecific artificial hybridization experiments have been conducted in our Akebia germplasm resources nursery.The results showed that there was no reproductive isolation between Akebia species,and fertile progeny could be produced.The synthesis of knowledge on these species provides insights for the rational development and utilization of these germplasm resources,and can facilitate the development of new breeding lines or varieties for commercial cultivation or production.Finally,perspectives on Akebia breeding research are discussed and conclusions are provided.This review provided breeders with new insights into Akebia domestication and breeding,and we also proposed five basic steps in the domestication of new fruit crops.

Recent progression and future perspectives in cotton genomic breeding

Upland cotton is an important global cash crop for its long seed fibers and high edible oil and protein content.Progress in cotton genomics promotes the advancement of cotton genetics,evolutionary studies,functional genetics,and breeding,and has ushered cotton research and breeding into a new era.Here,we summarize high-impact genomics studies for cotton from the last 10 years.The diploid Gossypium arboreum and allotetraploid Gossypium hirsutum are the main focus of most genetic and genomic studies.We next review recent progress in cotton molecular biology and genetics,which builds on cotton genome sequencing efforts,population studies,and functional genomics,to provide insights into the mechanisms shaping abiotic and biotic stress tolerance,plant architecture,seed oil content,and fiber development.We also suggest the application of novel technologies and strategies to facilitate genome-based crop breeding.Explosive growth in the amount of novel genomic data,identified genes,gene modules,and pathways is now enabling researchers to utilize multidisciplinary genomics-enabled breeding strategies to cultivate"super cotton",synergistically improving multiple traits.These strategies must rise to meet urgent demands for a sustainable cotton industry.

Breeding strategies for increasing yield potential in super hybrid rice

Super hybrid rice breeding is a new breeding method combining semi-dwarf breeding and heterosis breeding using germplasm and gene-environment interactions.This paper reviews the breeding strategies of super hybrid rice breeding in China,focusing on the utilization of heterosis of indica and japonica subspecies,construction of ideal plant architecture and pyramiding of disease resistant genes in restorer lines.To develop super hybrid rice,considerable effort should be made to explore genes related with high yield,good quality,resistance to pests and diseases,tolerance to stresses.Molecular breeding methods in combination with crossing techniques should be adopted in super hybrid rice breeding.

ROLE OF NITROGEN SENSING AND ITS INTEGRATIVE SIGNALING PATHWAYS IN SHAPING ROOT SYSTEM ARCHITECTURE

The Green Revolution of the 1960s boosted crop yields in part through widespread production of semidwarf plant cultivars and extensive use of mineral fertilizers.The beneficial semidwarfism of cereal Green Revolution cultivars is due to the accumulation of plant growth-repressing DELLA proteins,which increases lodging resistance but requires a high-nitrogen fertilizer to obtain high yield.Given that environmentally degrading fertilizer use underpins current worldwide crop production,future agricultural sustainability needs a sustainable Green Revolution through reducing N fertilizer use while boosting grain yield above what is currently achievable.Despite a great deal of research efforts,only a few genes have been demonstrated to improve N-use efficiency in crops.The molecular mechanisms underlying the coordination between plant growth and N metabolism is still not fully understood,thus preventing significant improvement.Recent advances of how plants sense,capture and respond to varying N supply in model plants have shed light on how to improve sustainable productivity in agriculture.This review focuses on the current understanding of root developmental and metabolic adaptations to N availability,and discuss the potential approaches to improve N-use efficiency in high-yielding cereal crops.

Improving coordination of plant growth and nitrogen metabolism for sustainable agriculture

The agricultural green revolution of the 1960s boosted cereal crop yield was in part due to cultivation of semi-dwarf green revolution varieties.The semi-dwarf plants resist lodging and require high nitrogen(N)fertilizer inputs to maximize yield.To produce higher grain yield,inorganic fertilizer has been overused by Chinese farmers in intensive crop production.With the ongoing increase in the food demand of global population and the environmental pollution,improving crop productivity with reduced N supply is a pressing challenge.Despite a great deal of research efforts,to date only a few genes that improve N use efficiency(NUE)have been identified.The molecular mechanisms underlying the coordination of plant growth,carbon(C)and N assimilation is still not fully understood,thus preventing significant improvement.Recent advances have shed light on how explore NUE within an overall plant biology system that considered the co-regulation of plant growth,C and N metabolisms as a whole,rather than focusing specifically on N uptake and assimilation.There are several potential approaches to improve NUE discussed in this review.Increasing knowledge of how plants sense and respond to changes in N availability,as well as identifying new targets for breeding strategies to simultaneously improve NUE and grain yield,could usher in a new green revolution.

Viability,behavior,and color expression in the offspring of matings between common wall lizard Podarcis muralis color morphs

Color polymorphisms are widely studied to identify the mechanisms responsible for the origin and maintenance of phenotypic variability in nature.Two of the mechanisms of balancing selection currently thought to explain the long-term persistence of polymorphisms are the evolution of alternative phenotypic optima through correlational selection on suites of traits including color and heterosis.Both of these mechanisms can generate differences in offspring viability and fitness arising from different morph combinations.Here,we examined the effect of parental morph combination on fertilization success,embryonic viability,newborn quality,antipredator,and foraging behavior,as well as inter-annual survival by conducting controlled matings in a polymorphic lacertid Podarcis muralis,where color morphs are frequently assumed to reflect alternative phenotypic optima(e.g.,alternative reproductive strategies).Juveniles were kept in outdoor tubs for a year in order to study inter-annual growth,survival,and morph inheritance.In agreement with a previous genome-wide association analysis,morph frequencies in the year-old juveniles matched the frequencies expected if orange and yellow expressions depended on recessive homozygosity at 2 separate loci.Our findings also agree with previous literature reporting higher reproductive output of heavy females and the higher overall viability of heavy newborn lizards,but we found no evidence for the existence of alternative breeding investment strategies in female morphs,or morphcombination effects on offspring viability and behavior.We conclude that inter-morph breeding remains entirely viable and genetic incompatibilities are of little significance for the maintenance of discrete color morphs in P.muralis from the Pyrenees.