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| 1 | Genetic basis and breeding application of clonal diversity and dual reproduction modes in polyploid Carassius auratus gibelio显示文摘A unisexual species is generally associated with polyploidy, and reproduced by a unisexual reproduction mode, such as gyno- genesis, hybridogenesis or parthenogenesis. Compared with other unisexual and polyploid species, gibel carp (Carassius au- ratus gibelio) has a higher ploidy level of hexaploid. It has undergone several successive rounds of genome polyploidy, and experienced an additional, more recent genome duplication event. More significantly, the dual reproduction modes, including gynogenesis and sexual reproduction, have been demonstrated to coexist in the polyploid gibel carp. This article reviews the genetic basis concerning polyploidy origin, clonal diversity and dual reproduction modes, and outlines the progress in new va- riety breeding and gene identification involved in the reproduction and early development. The data suggests that gibel carp are under an evolutionary trajectory of diploidization. As a novel evolutionary developmental (Evo-Devo) biology model, this work highlights future perspectives about the functional divergence of duplicated genes and the sexual origin of vertebrate animals. | GUI JianFang* & ZHOU Li State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China | 2010 | Science China(Life Sciences)2010，53，4： | 62 |
| 2 | Breeding high-yield superior quality hybrid super rice by rational design显示文摘The challenge of meeting the increasing demand for worldwide rice production has driven a sustained quest for advances in rice breeding for yield. Two breakthroughs that led to quantum leaps in productivity last century were the introduction of semidwarf varieties and of hybrid rice. Subsequent gains in yield have been incremental. The next major leap in rice breeding is now upon us through the application of rational design to create defined ideotypes. The exploitation of wide-cross compatibility and intersubspecific heterosis,combined with rapid genome sequencing and the molecular identification of genes for major yield and quality traits have now unlocked the potential for rational design. | Qian Qian Longbiao Guo Steven M.Smith Jiayang Li | 2016 | National Science Review2016，3，3： | 48 |
| 3 | Distant hybridization leads to different ploidy fishes显示文摘Distant hybridization makes it possible to transfer the genome of one species to another, which results in changes in phenotypes and genotypes of the progenies. This study shows that distant hybridization or the combination of this method with gynogenesis or androgenesis lead to different ploidy fishes with genetic variation, including fertile tetraploid hybrids, sterile triploid hybrids, fertile diploid hybrids, fertile diploid gynogenetic fish, and their derived progenies. The formations of the different ploidy fishes depend on the genetic relationship between the parents. In this study, several types of distant hybridization, including red crucian carp (Carassius auratus red var.) (2n=100, abbreviated as RCC) (♀)×common carp (Cyprinus carpio L.) (2n=100, abbreviated as CC) (♂), and RCC (2n=100) (♀)×blunt snout bream (Megalobrama amblycephala) (2n=48, abbreviated as BSB) (♂) are described. In the distant hybridization of RCC (♀)×CC (♂), bisexual fertile F3–F18 allotetraploid hybrids (4n=200, abbreviated as 4nAT) were formed. The diploid hybrid eggs and diploid sperm generated by the females and males of 4nAT developed into diploid gynogenetic hybrids and diploid androgenetic hybrids, respectively, by gynogenesis and androgenesis, without treatment for doubling the chromosome. Improved tetraploid hybrids and improved diploid fishes with genetic variation were derived from the gynogenetic hybrid line. The improved diploid fishes included the high-body RCC and high-body goldfish. The formation of the tetraploid hybrids was related to the occurrence of unreduced gametes generated from the diploid hybrids, which involved in premeiotic endoreduplication, endomitosis, or fusion of germ cells. The sterile triploid hybrids (3n=150) were produced on a large scale by crossing the males of tetraploid hybrids with females of diploid fish (2n=100). In another distant hybridization of RCC (♀)×BSB (♂), different ploidy fishes were obtained, including diploid bisexual fertile natural gynogenetic fish (2n=100), sterile triploid hybrids (3n=124), and bisexual fertile tetraploid hybrids (4n=148). Furthermore, two kinds of pentaploid hybrids (5n=172 and 5n=198) were formed. The biological characteristics and the mechanisms of formation of the different ploidy fish were compared and discussed at the cellular and molecular level. The results indicated distant hybridization or the combination of this method with gynogenesis or androgenesis affects the formation of different ploidy fish with genetic variation. | LIU ShaoJun Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha 410081, China | 2010 | Science China(Life Sciences)2010，53，4： | 39 |
| 4 | Production and genetic improvement of minor cereals in China显示文摘China is a leading country in the production of several minor cereals such as foxtail millet,Job's tears,naked oat,and naked barley.Sorghum and proso millet have also contributed greatly to Chinese agriculture.Foxtail millet,sorghum,barley,and proso millet were widely grown as major crops 60 years ago,and the reduction in their cultivation area reflects historical changes in Chinese agriculture over the past decades.Systematic germplasm collections from the 1950 s to the 1990 s gathered more than 66,690 accessions of these minor cereals,and for some of them,the Chinese germplasm collections are the largest in the world;for example,the 27,700 accessions of foxtail millet.Germplasm evaluations of each cereal species have focused mainly on drought tolerance,nutritional quality,and resistance to their main diseases.Comparisons among lines and selection of those with desirable traits were the main breeding methods for minor cereals in the 1950 s and 1960 s,but these methods were replaced by crossbreeding in the 1970 s.Newly developed cultivars have greatly changed the production situation,and many super cultivars have become milestones in crop breeding history.In this review,we describe the distribution and ecoregions,origin and domestication,and landmark varieties of several minor cereals in China.Nearly all of the minor cereals are drought-tolerant and fertilizer-efficient.The requirements for environmentally friendly crops and a more diverse food supply for humans and animals provide new opportunities to cultivate minor cereals in the drier and warmer environmental conditions that are predicted in the future. | Xianmin Diao | 2017 | The Crop Journal2017，5，2： | 38 |
| 5 | Development of a Haploid-Inducer Mediated Genome Editing System for Accelerating Maize Breeding显示文摘Crop breeding aims to generate pure in bred lines with multiple desired traits. Doubled haploid (DH) and genome editing using CRISPR/Cas9 are two powerful game-changing technologies in crop breeding. However, both of them still fall short for rapid generation of pure elite lines with integrated favorable traits. Here, we report the development of a Haploid-Inducer Mediated Genome Editing (IMGE) approach, which utilizes a maize haploid inducer line carrying a CRISPR/Cas9 cassette targeting for a desired agronomic trait to pollinate an elite maize in bred line and to generate genome-edited haploids in the elite maize background. Homozygous pure DH lines with the desired trait improvement could be generated within two generations, thus bypassing the lengthy procedure of repeated crossing and backcrossing used in conventional breeding for integrating a desirable trait into elite commercial backgrounds. | Baobao Wang Lei Zhu Binbin Zhao Yongping Zhao Yurong Xie Zhigang Zheng Yaoyao Li Juan Sun Haiyang Wang | 2019 | Molecular Plant2019，12，4： | 32 |
| 6 | Development of japonica Photo-Sensitive Genic Male Sterile Rice Lines by Editing Carbon Starved Anther Using CRISPR/Cas9显示文摘Rice is one of the most important crops as it supports over25%of total caloric intake for humans(Kusano et al.,2015).The world population reached 7.3 billion in 2015 and is projected to reach 8.5 billion in 2030(Word Population Prospects:2015 Revision).To meet the food demands for the everincreasing population with limited arable land,scarce | Quanlin Li Dabing Zhang Mingjiao Chen Wanqi Liang Jiaojun Wei Yiping Qi Zheng Yuan | 2016 | Journal of Genetics and Genomics2016，43，6： | 26 |
| 7 | Rapeseed research and production in China显示文摘Rapeseed(Brassica napus L.) is the largest oilseed crop in China and accounts for about 20% of world production.For the last 10 years,the production,planting area,and yield of rapeseed have been stable,with improvement of seed quality and especially seed oil content.China is among the leading countries in rapeseed genomic research internationally,having jointly with other countries accomplished the whole genome sequencing of rapeseed and its two parental species,Brassica oleracea and Brassica rapa.Progress on functional genomics including the identification of QTL governing important agronomic traits such as yield,seed oil content,fertility regulation,disease and insect resistance,abiotic stress,nutrition use efficiency,and pod shattering resistance has been achieved.As a consequence,molecular markers have been developed and used in breeding programs.During 2005–2014,215 rapeseed varieties were registered nationally,including 210 winter-and 5 spring-type varieties.Mechanization across the whole process of rapeseed production was investigated and operating instructions for all relevant techniques were published.Modern techniques for rapeseed field management such as high-density planting,controlled-release fertilizer,and biocontrol of disease and pests combined with precision tools such as drones have been developed and are being adopted in China.With the application of advanced breeding and production technologies,in the near future,the oil yield and quality of rapeseed varieties will be greatly increased,and more varieties with desirable traits,especially early maturation,high yield,high resistance to biotic and abiotic stress,and suitability for mechanized harvesting will be developed.Application of modern technologies on the mechanized management of rapeseed will greatly increase grower profit. | Qiong Hu Wei Hua Yan Yin Xuekun Zhang Lijiang Liu Jiaqin Shi Yongguo Zhao Lu Qin Chang Chen Hanzhong Wang | 2017 | The Crop Journal2017，5，2： | 25 |
| 8 | Research progress on plant tolerance to soil salinity and alkalinity in sorghum显示文摘Sorghum is an important source of food, feed and raw material for brewing, and is expected to be a promising bioenergy crop. Sorghum is well known for its strong resistance to abiotic stress and wide adaptability, and salt tolerance is one of its main characteristics. Increasing sorghum planting acreage on saline-alkalien land is one way to effectively use this kind of marginal soil. In this paper, domestic and overseas research on plant tolerance to soil salinity and alkalinity in sorghum, including salt-tolerant genetics and breeding, physiology, cultivation, and identification of tolerant germplasms, are reviewed. Suggestions for further studies on salinity and alkalinity tolerance in sorghum are given, and the prospects for sorghum production in saline-alkalien land are discussed. | HUANG Rui-dong | 2018 | Journal of Integrative Agriculture2018，17，4： | 25 |
| 9 | Grain quality changes and responses to nitrogen fertilizer of japonica rice cultivars released in the Yangtze River Basin from the 1950s to 2000s显示文摘While the yield potential of rice has increased but little is known about the impact of breeding on grain quality, especially under different levels of N availability. In order to investigate the integrated effects of breeding and N levels on rice quality 12 japonica rice cultivars bred in the past60 years in the Yangtze River Basin were used with three levels of N: 0 kg N ha-1, 240 kg N ha-1,and 360 kg N ha-1. During the period, milling quality(brown rice percentage, milled rice percentage, and head rice percentage), appearance quality(chalky kernels percentage, chalky size, and chalkiness), and eating and cooking quality(amylose content, gel consistency, peak viscosity, breakdown, and setback) were significantly improved, but the nutritive value of the grain has declined due to a reduction in protein content. Micronutrients, such as Cu, Mg, and S contents, were decreased, and Fe, Mn, Zn, Na, Ca, K, P, B contents were increased. These changes in grain quality imply that simultaneous improvements in grain yield and grain quality are possible through selection. Overall, application of N fertilizer decreased grain quality, especially in terms of eating and cooking quality. Under higher N levels, higher protein content was the main reason for deterioration of grain quality, although lower amylose content might contribute to improving starch pasting properties. These results suggest that further improvement in grain quality will depend on both breeding and cultivation practices, especially in regard to nitrogen and water management. | Junfei Gu Jing Chen Lu Chen Zhiqin Wang Hao Zhang Jianchang Yang | 2015 | The Crop Journal2015，3，4： | 25 |
| 10 | Diverse and variable sex determination mechanisms in vertebrates显示文摘Sex is prevalent in nature and sex determination is one of the most fundamental biological processes, while the way of initiating female and male development exhibits remarkable diversity and variability across vertebrates. The knowledge on why and how sex determination mechanisms evolve unusual plasticity remains limited. Here, we summarize sex determination systems,master sex-determining genes and gene-regulatory networks among vertebrates. Recent research advancements on sex determination system transition are also introduced and discussed in some non-model animals with multiple sex determination mechanisms. This review will provide insights into the origin, transition and evolutionary adaption of different sex determination strategies in vertebrates, as well as clues for future perspectives in this field. | Xi-Yin Li Jian-Fang Gui | 2018 | Science China(Life Sciences)2018，61，12： | 20 |
| 11 | Perspectives on the Application of Genome-Editing Technologies in Crop Breeding显示文摘Most conventional and modern crop-improvement methods exploit natural or artificially induced genetic variations and require laborious characterization of the progenies of multiple generations derived from time-consuming genetic crosses.Genome-editing systems,in contrast,provide the means to rapidly modify genomes in a precise and predictable way,making it possible to introduce improvements directly into elite varieties.Here,we describe the range of applications available to agricultural researchers using existing genome-editing tools.In addition to providing examples of genome-editing applications in crop breeding,we discuss the technical and social challenges faced by breeders using genome-editing tools for crop improvement. | Kai Hua Jinshan Zhang Jose Ramon Botella Changle Ma Fanjiang Kong Baohui Liu Jian-Kang Zhu | 2019 | Molecular Plant2019，12，8： | 19 |
| 12 | Breeding better cultivars,faster:applications of new technologies for the rapid deployment of superior horticultural tree crops显示文摘Woody perennial plants,including trees that produce fruits and nuts of horticultural value,typically have long breeding cycles,and development and introduction of improved cultivars by plant breeders may require many breeding cycles and dozens of years.However,recent advances in biotechnologies and genomics have the potential to accelerate cultivar development greatly in all crops.This mini-review summarizes approaches to reduce the number and the duration of breeding cycles for horticultural tree crops,and outlines the challenges that remain to implement these into efficient breeding pipelines. | Steve van Nocker Susan E Gardiner | 2014 | Horticulture Research2014，1，1： | 19 |
| 13 | Gene editing in plants:progress and challenges显示文摘The clustered regularly interspaced short palindromic repeat(CRISPR)-associated protein 9(Cas9)genome editing system is a powerful tool for targeted gene modifications in a wide range of species,including plants.Over the last few years,this system has revolutionized the way scientists perform genetic studies and crop breeding,due to its simplicity,flexibility,consistency and high efficiency.Considerable progress has been made in optimizing CRISPR/Cas9 systems in plants,particularly for targeted gene mutagenesis.However,there are still a number of important challenges ahead,including methods for the efficient delivery of CRISPR and other editing tools to most plants,and more effective strategies for sequence knock-ins and replacements.We provide our viewpoint on the goals,potential concerns and future challenges for the development and application of plant genome editing tools. | Yanfei Mao Jose Ramon Botella Yaoguang Liu Jian-Kang Zhu | 2019 | National Science Review2019，6，3： | 17 |
| 14 | Plant Phenotyping:Past,Present,and Future显示文摘A plant develops the dynamic phenotypes from the interaction of the plant with the environment.Understanding these processes that span plant’s lifetime in a permanently changing environment is essential for the advancement of basic plant science and its translation into application including breeding and crop management.The plant research community was thus confronted with the need to accurately measure diverse traits of an increasingly large number of plants to help plants to adapt to resource-limiting environment and low-input agriculture.In this overview,we outline the development of plant phenotyping as a multidisciplinary field.We sketch the technological advancement that laid the foundation for the development of phenotyping centers and evaluate the upcoming challenges for further advancement of plant phenotyping specifically with respect to standardization of data acquisition and reusability.Finally,we describe the development of the plant phenotyping community as an essential step to integrate the community and effectively use the emerging synergies. | Roland Pieruschka Uli Schurr | 2019 | Plant Phenomics2019，1，1： | 17 |
| 15 | The chromosome-scale genome reveals the evolution and diversification after the recent tetraploidization event in tea plant显示文摘Tea is one of the most popular nonalcoholic beverages due to its characteristic secondary metabolites with numerous health benefits.Although two draft genomes of tea plant(Camellia sinensis)have been published recently,the lack of chromosome-scale assembly hampers the understanding of the fundamental genomic architecture of tea plant and potential improvement.Here,we performed a genome-wide chromosome conformation capture technique(Hi-C)to obtain a chromosome-scale assembly based on the draft genome of C.sinensis var.sinensis and successfully ordered 2984.7 Mb(94.7%)scaffolds into 15 chromosomes.The scaffold N50 of the improved genome was 218.1 Mb,~157-fold higher than that of the draft genome.Collinearity comparison of genome sequences and two genetic maps validated the high contiguity and accuracy of the chromosome-scale assembly.We clarified that only one Camellia recent tetraploidization event(CRT,58.9–61.7 million years ago(Mya))occurred after the core-eudicot common hexaploidization event(146.6–152.7 Mya).Meanwhile,9243 genes(28.6%)occurred in tandem duplication,and most of these expanded after the CRT event.These gene duplicates increased functionally divergent genes that play important roles in tea-specific biosynthesis or stress response.Sixty-four catechin-and caffeine-related quantitative trait loci(QTLs)were anchored to chromosome assembly.Of these,two catechin-related QTL hotspots were derived from the CRT event,which illustrated that polyploidy has played a dramatic role in the diversification of tea germplasms.The availability of a chromosome-scale genome of tea plant holds great promise for the understanding of genome evolution and the discovery of novel genes contributing to agronomically beneficial traits in future breeding programs. | Jie-Dan Chen Chao Zheng Jian-Qiang Ma Chen-Kai Jiang Sezai Ercisli Ming-Zhe Yao Liang Chen | 2020 | Horticulture Research2020，7，1： | 17 |
| 16 | Retrospective and perspective of rice breeding in China显示文摘Breeding is the art and science of selecting and changing crop traits for the benefit of human beings. For several decades, tremendous efforts have been made by Chinese scientists in rice breeding in improving grain yield, nutrition quality, and environmental performance, achieving substantial progress for global food security. Several generations of crop breeding technologies have been developed, for example,selection of better performance in the field among variants(conventional breeding), application of molecular markers for precise selection(molecular marker assisted breeding), and development of molecular design(molecular breeding by rational design). In this review, we briefly summarize the advances in conventional breeding, functional genomics for genes and networks in rice that regulate important agronomic traits, and molecular breeding in China with focuses on high yield, good quality,stress tolerance, and high nutrient-use efficiency. These findings have paved a new avenue for rational design of crops to develop ideal varieties with super performance and productivity. | Shiwei Bai Hong Yu Bing Wang Jiayang Li | 2018 | Journal of Genetics and Genomics2018，45，11： | 16 |
| 17 | Wheat breeding in northern China: Achievements and technical advances显示文摘Common wheat is the major cereal crop that underpins the food safety of China. Both winter wheat and spring wheat are grown on ~24 million ha. This review aims to summarize the current status of wheat production and breeding progress in the northern wheat production areas of the country, and to review recently advanced technologies being applied in wheat breeding, including the use of dwarf-male-sterile(DMS) wheat, speed breeding and specialized wheat breeding SNP chips. Crossing is the initial step in most breeding programs. DMS wheat is a convenient tool for large scale production of hybrid seed. Speed breeding or accelerated generation turnover attempts to reduce the time taken in cultivar development. Several different SNP chips are high-throughput, genome-wide genotyping platforms for breeding and research. | Hongjie Li Yang Zhou Wenli Xin Yiqin Wei Junling Zhang Lilei Guo | 2019 | The Crop Journal2019，7，6： | 16 |
| 18 | A Weakly Supervised Deep Learning Framework for Sorghum Head Detection and Counting显示文摘The yield of cereal crops such as sorghum(Sorghum bicolor L.Moench)depends on the distribution of crop-heads in varying branching arrangements.Therefore,counting the head number per unit area is critical for plant breeders to correlate with the genotypic variation in a specific breeding field.However,measuring such phenotypic traitsmanually is an extremely labor-intensive process and suffers from low efficiency and human errors.Moreover,the process is almost infeasible for large-scale breeding plantations or experiments.Machine learning-based approaches like deep convolutional neural network(CNN)based object detectors are promising tools for efficient object detection and counting.However,a significant limitation of such deep learningbased approaches is that they typically require a massive amount of hand-labeled images for training,which is still a tedious process.Here,we propose an active learning inspired weakly supervised deep learning framework for sorghum head detection and counting from UAV-based images.We demonstrate that it is possible to significantly reduce human labeling effort without compromising final model performance(��2 between human count and machine count is 0.88)by using a semitrained CNN model(i.e.,trained with limited labeled data)to perform synthetic annotation.In addition,we also visualize key features that the network learns.This improves trustworthiness by enabling users to better understand and trust the decisions that the trained deep learning model makes. | Sambuddha Ghosal Bangyou Zheng Scott CChapman Andries BPotgieter David RJordan Xuemin Wang Asheesh KSingh Arti Singh Masayuki Hirafuji Seishi Ninomiya Baskar Ganapathysubramanian Soumik Sarkar Wei Guo | 2019 | Plant Phenomics2019，1，1： | 16 |
| 19 | The genome sequence of celery(Apium graveolens L.),an important leaf vegetable crop rich in apigenin in the Apiaceae family显示文摘Celery(Apium graveolens L.)is a vegetable crop in the Apiaceae family that is widely cultivated and consumed because it contains necessary nutrients and multiple biologically active ingredients,such as apigenin and terpenoids.Here,we report the genome sequence of celery based on the use of HiSeq 2000 sequencing technology to obtain 600.8 Gb of data,achieving~189-fold genome coverage,from 68 sequencing libraries with different insert sizes ranging from 180 bp to 10 kb in length.The assembled genome has a total sequence length of 2.21 Gb and consists of 34,277 predicted genes.Repetitive DNA sequences represent 68.88%of the genome sequences,and LTR retrotransposons are the main components of the repetitive sequences.Evolutionary analysis showed that a recent whole-genome duplication event may have occurred in celery,which could have contributed to its large genome size.The genome sequence of celery allowed us to identify agronomically important genes involved in disease resistance,flavonoid biosynthesis,terpenoid metabolism,and other important cellular processes.The comparative analysis of apigenin biosynthesis genes among species might explain the high apigenin content of celery.The whole-genome sequences of celery have been deposited at CeleryDB(http://gffzz7798edb5f31c4ba3hqf090kokff5n6566.ffgz.tsg.suse.edu.cn/celerydb).The availability of the celery genome data advances our knowledge of the genetic evolution of celery and will contribute to further biological research and breeding in celery as well as other Apiaceae plants. | Meng-Yao Li Kai Feng Xi-Lin Hou Qian Jiang Zhi-Sheng Xu Guang-Long Wang Jie-Xia Liu Feng Wang Ai-Sheng Xiong | 2020 | Horticulture Research2020，7，1： | 16 |
| 20 | Advances and prospects of super rice breeding in China显示文摘Super rice breeding in China has been very successful over the past 3 decades, and the Chinese government has made great efforts to support breeding and cultivation of both conventional and hybrid super rice. In this review, we focus on the progress in and potential of super rice breeding. After the establishment of the breeding theory and strategy of 'generating an ideotype with strong heterosis through inter-subspecies hybridization, by using gene pyramiding to combine elite traits through composite-crossing to breed super rice varieties with both ideotype and strong hybrid vigor', a series of major breakthroughs have been achieved in both conventional and super hybrid rice breeding. A number of new genetic materials with ideotype have been created successfully, and the Ministry of Agriculture of China has approved 156 novel super rice varieties and combinations for commercialization. During the Developing the Super Rice Varieties Program, great attention has also been paid to the integration and demonstration of the rice production technology. Collaboration between industry and university researchers has led to technological innovations and initiation of a demonstration system for super hybrid rice. With widespread cultivation of super rice with higher quality and yield, as well as resistance or tolerance to abiotic or biotic stresses, the yield of rice production per unit has reached a new level. In addition to increased quality and yield, hybrid rice breeding has also led to improvements in many other agronomic traits, such as resistance to pests and diseases, resistance to lodging, and optimized light distribution in population. Achievements in super rice breeding and innovation in rice production have made major contributions to the progress in rice sciences and worldwide food security. | TANG Liang XU Zheng-jin CHEN Wen-fu | 2017 | Journal of Integrative Agriculture2017，16，5： | 14 |
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