Rujia Chen, Ning Xiao, Yue Lu, Tianyun Tao, Qianfeng Huang, Shuting Wang, Zhichao Wang, Mingli Chuan, Qing Bu, Zhou Lu, Hanyao Wang, Yanze Su, Yi Ji, Jianheng Ding, Ahmed Gharib, Huixin Liu, Yong Zhou, Shuzhu Tang, Guohua Liang, Honggen Zhang, Chuandeng Yi, Xiaoming Zheng, Zhukuan Cheng, Yang Xu, Pengcheng Li, Chenwu Xu, Jinling Huang, Aihong Li, Zefeng Yang <<<

The role of de novo evolved genes from non-coding sequences in regulating morphological differentiation between species/subspecies remains largely unknown. Here, we show that a rice de novo gene GSE9 contributes to grain shape difference between indica/xian and japonica/geng varieties. GSE9 evolves from a previous non-coding region of wild rice Oryza rufipogon through the acquisition of start codon. This gene is inherited by most japonica varieties, while the original sequence (absence of start codon, gse9) is present in majority of indica varieties. Knockout of GSE9 in japonica varieties leads to slender grains, whereas introgression to indica background results in round grains. Population evolutionary analyses reveal that gse9 and GSE9 are derived from wild rice Or-I and Or-III groups, respectively. Our findings uncover that the de novo GSE9 gene contributes to the genetic and morphological divergence between indica and japonica subspecies, and provide a target for precise manipulation of rice grain shape. <<<

Jianqing Niu, Shengwei Ma, Shusong Zheng, Chi Zhang, Yaru Lu, Yaoqi Si, Shuiquan Tian, Xiaoli Shi, Xiaolin Liu, Muhammad Kashif Naeem, Hua Sun, Yafei Hu, Huilan Wu, Yan Cui, Chunlin Chen, Wenbo Long, Yue Zhang, Mengjun Gu, Man Cui, Qiao Lu, Wenjuan Zhou, Junhua Peng, Eduard Akhunov, Fei He, Shancen Zhao, Hong-Qing Ling <<<

Breeding has dramatically changed the plant architecture of wheat (Triticum aestivum), resulting in the development of high-yielding varieties adapted to modern farming systems. However, how wheat breeding shaped the genomic architecture of this crop remains poorly understood. Here, we performed a comprehensive comparative analysis of a whole-genome resequencing panel of 355 common wheat accessions (representing diverse landraces and modern cultivars from China and the United States) at the phenotypic and genomic levels. The genetic diversity of modern wheat cultivars was clearly reduced compared to landraces. Consistent with these genetic changes, most phenotypes of cultivars from China and the United States were significantly altered. Of the 21 agronomic traits investigated, 8 showed convergent changes between the 2 countries. Moreover, of the 207 loci associated with these 21 traits, more than half overlapped with genomic regions that showed evidence of selection. The distribution of selected loci between the Chinese and American cultivars suggests that breeding for increased productivity in these 2 regions was accomplished by pyramiding both shared and region-specific variants. This work provides a framework to understand the genetic architecture of the adaptation of wheat to diverse agricultural production environments, as well as guidelines for optimizing breeding strategies to design better wheat varieties. <<<

Daiqi Wang, Hongru Wang, Xiaomei Xu, Man Wang, Yahuan Wang, Hong Chen, Fei Ping, Huanhuan Zhong, Zhengkun Mu, Wantong Xie, Xiangyu Li, Jingbin Feng, Milan Zhang, Zhilan Fan, Tifeng Yang, Junliang Zhao, Bin Liu, Ying Ruan, Guiquan Zhang, Chunlin Liu, Ziqiang Liu <<<

Understanding the evolutionary forces in speciation is a central goal in evolutionary biology. Asian cultivated rice has two subspecies, indica and japonica, but the underlying mechanism of the partial reproductive isolation between them remains obscure. Here we show a presence-absence variation (PAV) at the Se locus functions as an indica-japonica reproductive barrier by causing hybrid sterility (HS) in indica-japonica crosses. The locus comprises two adjacent genes: ORF3 encodes a sporophytic pollen killer, whereas ORF4 protects pollen in a gametophytic manner. In F of indica-japonica crosses, pollen with the japonica haplotype, which lacks the sequence containing the protective ORF4, is aborted due to the pollen-killing effect of ORF3 from indica. Evolutionary analysis suggests ORF3 is a gene associated with the Asian cultivated rice species complex, and the PAV has contributed to the reproductive isolation between the two subspecies of Asian cultivated rice. Our analyses provide perspectives on rice inter-subspecies post-zygotic isolation, and will promote efforts to overcome reproductive barriers in indica-japonica hybrid rice breeding. <<<

Long Li, Zhitao Tian, Jie Chen, Zengdong Tan, Yuting Zhang, Hu Zhao, Xiaowei Wu, Xuan Yao, Weiwei Wen, Wei Chen, Liang Guo <<<

BACKGROUND: Seed oil content is an important agronomic trait of Brassica napus (B. napus), and metabolites are considered as the bridge between genotype and phenotype for physical traits.RESULTS: Using a widely targeted metabolomics analysis in a natural population of 388 B. napus inbred lines, we quantify 2172 metabolites in mature seeds by liquid chromatography mass spectrometry, in which 131 marker metabolites are identified to be correlated with seed oil content. These metabolites are then selected for further metabolite genome-wide association study and metabolite transcriptome-wide association study. Combined with weighted correlation network analysis, we construct a triple relationship network, which includes 21,000 edges and 4384 nodes among metabolites, metabolite quantitative trait loci, genes, and co-expression modules. We validate the function of BnaA03.TT4, BnaC02.TT4, and BnaC05.UK, three candidate genes predicted by multi-omics analysis, which show significant impacts on seed oil content through regulating flavonoid metabolism in B. napus.CONCLUSIONS: This study demonstrates the advantage of utilizing marker metabolites integrated with multi-omics analysis to dissect the genetic basis of agronomic traits in crops. <<<

Development of wheat ( L) grain mainly depends on the processes of starch synthesis and storage protein accumulation, which are critical for grain yield and quality. However, the regulatory network underlying the transcriptional and physiological changes of grain development is still not clear. Here, we combined ATAC-seq and RNA-seq to discover the chromatin accessibility and gene expression dynamics during these processes. We found that the chromatin accessibility changes are tightly associated with differential transcriptomic expressions, and the proportion of distal ACRs was increased gradually during grain development. Specific transcription factor (TF) binding sites were enriched at different stages and were diversified among the 3 subgenomes. We further predicted the potential interactions between key TFs and genes related with starch and storage protein biosynthesis and found different copies of some key TFs played diversified roles. Overall, our findings have provided numerous resources and illustrated the regulatory network during wheat grain development, which would shed light on the improvement of wheat yields and qualities. <<<

Long Song, Jie Liu, Beilu Cao, Bin Liu, Xiaoping Zhang, Zhaoyan Chen, Chaoqun Dong, Xiangqing Liu, Zhaoheng Zhang, Wenxi Wang, Lingling Chai, Jing Liu, Jun Zhu, Shubin Cui, Fei He, Huiru Peng, Zhaorong Hu, Zhenqi Su, Weilong Guo, Mingming Xin, Yingyin Yao, Yong Yan, Yinming Song, Guihua Bai, Qixin Sun, Zhongfu Ni <<<

Modern green revolution varieties of wheat (Triticum aestivum L.) confer semi-dwarf and lodging-resistant plant architecture owing to the Reduced height-B1b (Rht-B1b) and Rht-D1b alleles. However, both Rht-B1b and Rht-D1b are gain-of-function mutant alleles encoding gibberellin signalling repressors that stably repress plant growth and negatively affect nitrogen-use efficiency and grain filling. Therefore, the green revolution varieties of wheat harbouring Rht-B1b or Rht-D1b usually produce smaller grain and require higher nitrogen fertilizer inputs to maintain their grain yields. Here we describe a strategy to design semi-dwarf wheat varieties without the need for Rht-B1b or Rht-D1b alleles. We discovered that absence of Rht-B1 and ZnF-B (encoding a RING-type E3 ligase) through a natural deletion of a haploblock of about 500 kilobases shaped semi-dwarf plants with more compact plant architecture and substantially improved grain yield (up to 15.2%) in field trials. Further genetic analysis confirmed that the deletion of ZnF-B induced the semi-dwarf trait in the absence of the Rht-B1b and Rht-D1b alleles through attenuating brassinosteroid (BR) perception. ZnF acts as a BR signalling activator to facilitate proteasomal destruction of the BR signalling repressor BRI1 kinase inhibitor 1 (TaBKI1), and loss of ZnF stabilizes TaBKI1 to block BR signalling transduction. Our findings not only identified a pivotal BR signalling modulator but also provided a creative strategy to design high-yield semi-dwarf wheat varieties by manipulating the BR signal pathway to sustain wheat production. <<<

Huili Zhang, Feifei Yu, Peng Xie, Shengyuan Sun, Xinhua Qiao, Sanyuan Tang, Chengxuan Chen, Sen Yang, Cuo Mei, Dekai Yang, Yaorong Wu, Ran Xia, Xu Li, Jun Lu, Yuxi Liu, Xiaowei Xie, Dongmei Ma, Xing Xu, Zhengwei Liang, Zhonghui Feng, Xiahe Huang, Hong Yu, Guifu Liu, Yingchun Wang, Jiayang Li, Qifa Zhang, Chang Chen, Yidan Ouyang, Qi Xie <<<

The use of alkaline salt lands for crop production is hindered by a scarcity of knowledge and breeding efforts for plant alkaline tolerance. Through genome association analysis of sorghum, a naturally high-alkaline-tolerant crop, we detected a major locus, (), specifically related to alkaline-salinity sensitivity. An allele with a carboxyl-terminal truncation increased sensitivity, whereas knockout of increased tolerance to alkalinity in sorghum, millet, rice, and maize. encodes an atypical G protein γ subunit that affects the phosphorylation of aquaporins to modulate the distribution of hydrogen peroxide (HO) These processes appear to protect plants against oxidative stress by alkali. Designing knockouts of homologs or selecting its natural nonfunctional alleles could improve crop productivity in sodic lands. <<<

Shogo Sato, Kenneth A Dyar, Jonas T Treebak, Sara L Jepsen, Amy M Ehrlich, Stephen P Ashcroft, Kajetan Trost, Thomas Kunzke, Verena M Prade, Lewin Small, Astrid Linde Basse, Milena Schönke, Siwei Chen, Muntaha Samad, Pierre Baldi, Romain Barrès, Axel Walch, Thomas Moritz, Jens J Holst, Dominik Lutter, Juleen R Zierath, Paolo Sassone-Corsi <<<

Tissue sensitivity and response to exercise vary according to the time of day and alignment of circadian clocks, but the optimal exercise time to elicit a desired metabolic outcome is not fully defined. To understand how tissues independently and collectively respond to timed exercise, we applied a systems biology approach. We mapped and compared global metabolite responses of seven different mouse tissues and serum after an acute exercise bout performed at different times of the day. Comparative analyses of intra- and inter-tissue metabolite dynamics, including temporal profiling and blood sampling across liver and hindlimb muscles, uncovered an unbiased view of local and systemic metabolic responses to exercise unique to time of day. This comprehensive atlas of exercise metabolism provides clarity and physiological context regarding the production and distribution of canonical and novel time-dependent exerkine metabolites, such as 2-hydroxybutyrate (2-HB), and reveals insight into the health-promoting benefits of exercise on metabolism. <<<

Baobao Wang, Mei Hou, Junpeng Shi, Lixia Ku, Wei Song, Chunhui Li, Qiang Ning, Xin Li, Changyu Li, Binbin Zhao, Ruyang Zhang, Hua Xu, Zhijing Bai, Zhanchao Xia, Hai Wang, Dexin Kong, Hongbin Wei, Yifeng Jing, Zhouyan Dai, Hu Hailing Wang, Xinyu Zhu, Chunhui Li, Xuan Sun, Shuaishuai Wang, Wen Yao, Gege Hou, Zhi Qi, He Dai, Xuming Li, Hongkun Zheng, Zuxin Zhang, Yu Li, Tianyu Wang, Taijiao Jiang, Zhaoman Wan, Yanhui Chen, Jiuran Zhao, Jinsheng Lai, Haiyang Wang <<<

Hybrid maize displays superior heterosis and contributes over 30% of total worldwide cereal production. However, the molecular mechanisms of heterosis remain obscure. Here we show that structural variants (SVs) between the parental lines have a predominant role underpinning maize heterosis. De novo assembly and analyses of 12 maize founder inbred lines (FILs) reveal abundant genetic variations among these FILs and, through expression quantitative trait loci and association analyses, we identify several SVs contributing to genomic and phenotypic differentiations of various heterotic groups. Using a set of 91 diallel-cross F hybrids, we found strong positive correlations between better-parent heterosis of the F hybrids and the numbers of SVs between the parental lines, providing concrete genomic support for a prevalent role of genetic complementation underlying heterosis. Further, we document evidence that SVs in both ZAR1 and ZmACO2 contribute to yield heterosis in an overdominance fashion. Our results should promote genomics-based breeding of hybrid maize. <<<

Yan Li, Yang Chen, Lu Zhou, Shengjie You, Heng Deng, Ya Chen, Saleh Alseekh, Yong Yuan, Rao Fu, Zixin Zhang, Dan Su, Alisdair R Fernie, Mondher Bouzayen, Tao Ma, Mingchun Liu, Yang Zhang <<<

Tomato (Solanum lycopersicum) is a major horticultural crop worldwide and has emerged as a preeminent model for metabolic research. Although many research efforts have focused on the analysis of metabolite differences between varieties and species, the dynamics of metabolic changes during the tomato growth cycle and the regulatory networks that underlie these changes are poorly understood. In this study, we integrated high-resolution spatio-temporal metabolome and transcriptome data to systematically explore the metabolic landscape across 20 major tomato tissues and growth stages. In the resulting MicroTom Metabolic Network, the 540 detected metabolites and their co-expressed genes could be divided into 10 distinct clusters based on their biological functions. Using this dataset, we constructed a global map of the major metabolic changes that occur throughout the tomato growth cycle and dissected the underlying regulatory network. In addition to verifying previously well-established regulatory networks for important metabolites, we identified novel transcription factors that regulate the biosynthesis of important secondary metabolites such as steroidal glycoalkaloids and flavonoids. Our findings provide insights into spatio-temporal changes in tomato metabolism and generate a valuable resource for the study of metabolic regulatory processes in model plants. <<<

Yongcai Huang, Haihai Wang, Yidong Zhu, Xing Huang, Shuai Li, Xingguo Wu, Yao Zhao, Zhigui Bao, Li Qin, Yongbo Jin, Yahui Cui, Guangjin Ma, Qiao Xiao, Qiong Wang, Jiechen Wang, Xuerong Yang, Hongjun Liu, Xiaoduo Lu, Brian A Larkins, Wenqin Wang, Yongrui Wu <<<

Teosinte, the wild ancestor of maize (Zea mays subsp. mays), has three times the seed protein content of most modern inbreds and hybrids, but the mechanisms that are responsible for this trait are unknown. Here we use trio binning to create a contiguous haplotype DNA sequence of a teosinte (Zea mays subsp. parviglumis) and, through map-based cloning, identify a major high-protein quantitative trait locus, TEOSINTE HIGH PROTEIN 9 (THP9), on chromosome 9. THP9 encodes an asparagine synthetase 4 enzyme that is highly expressed in teosinte, but not in the B73 inbred, in which a deletion in the tenth intron of THP9-B73 causes incorrect splicing of THP9-B73 transcripts. Transgenic expression of THP9-teosinte in B73 significantly increased the seed protein content. Introgression of THP9-teosinte into modern maize inbreds and hybrids greatly enhanced the accumulation of free amino acids, especially asparagine, throughout the plant, and increased seed protein content without affecting yield. THP9-teosinte seems to increase nitrogen-use efficiency, which is important for promoting a high yield under low-nitrogen conditions. <<<

Identification of alleles that improve crop production and lead to higher-yielding varieties are needed for food security. Here we show that the quantitative trait locus WFP (WEALTHY FARMER'S PANICLE) encodes OsSPL14 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 14, also known as IPA1). Higher expression of OsSPL14 in the reproductive stage promotes panicle branching and higher grain yield in rice. OsSPL14 controls shoot branching in the vegetative stage and is affected by microRNA excision. We also demonstrate the feasibility of using the OsSLP14(WFP) allele to increase rice crop yield. Introduction of the high-yielding OsSPL14(WFP) allele into the standard rice variety Nipponbare resulted in increased rice production. <<<

Jinrong Peng , Donald E. Richards , Nigel M. Hartley , George P. Murphy , Katrien M. Devos , John E. Flintham , James Beales , Leslie J. Fish , Anthony J. Worland , Fatima Pelica , Duraialagaraja Sudhakar , Paul Christou , John W. Snape , Michael D. Gale , Nicholas P. Harberd <<<

World wheat grain yields increased substantially in the 1960s and 1970s because farmers rapidly adopted the new varieties and cultivation methods of the so-called ‘green revolution’1,2,3,4. The new varieties are shorter, increase grain yield at the expense of straw biomass, and are more resistant to damage by wind and rain3,4. These wheats are short because they respond abnormally to the plant growth hormone gibberellin. This reduced response to gibberellin is conferred by mutant dwarfing alleles at one of two Reduced height-1 (Rht-B1 and Rht-D1) loci4,5. Here we show that Rht-B1/Rht-D1 and maize dwarf-8 (d8)6,7 are orthologues of the Arabidopsis Gibberellin Insensitive (GAI) gene8,9. These genes encode proteins that resemble nuclear transcription factors and contain an SH2-like10 domain, indicating that phosphotyrosine may participate in gibberellin signalling. Six different orthologous dwarfing mutant alleles encode proteins that are altered in a conserved amino-terminal gibberellin signalling domain. Transgenic rice plants containing a mutant GAI allele give reduced responses to gibberellin and are dwarfed, indicating that mutant GAI orthologues could be used to increase yield in a wide range of crop species. <<<

As a major event in human civilization, wild plants were successfully domesticated to be crops, largely owing to continuing artificial selection. Here, we summarize new discoveries made during the past decade in crop domestication and breeding. The construction of crop genome maps and the functional characterization of numerous trait genes provide foundational information. Approaches to read, interpret, and write complex genetic information are being leveraged in many plants for highly efficient de novo or re-domestication. Understanding the underlying mechanisms of crop microevolution and applying the knowledge to agricultural productions will give possible solutions for future challenges in food security. <<<

Flowering plants alternate between multicellular haploid (gametophyte) and diploid (sporophyte) generations. Pollen actively transcribes its haploid genome, providing phenotypic diversity even among pollen grains from a single plant. In this study, we used allele-specific RNA sequencing of single pollen precursors to follow the shift to haploid expression in maize pollen. We observed widespread biallelic expression for 11 days after meiosis, indicating that transcripts synthesized by the diploid sporophyte persist long into the haploid phase. Subsequently, there was a rapid and global conversion to monoallelic expression at pollen mitosis I, driven by active new transcription from the haploid genome. Genes showed evidence of increased purifying selection if they were expressed after (but not before) pollen mitosis I. This work establishes the timing during which haploid selection may act in pollen. <<<

Yongqiang Liu, Hongru Wang, Zhimin Jiang, Wei Wang, Ruineng Xu, Qihui Wang, Zhihua Zhang, Aifu Li, Yan Liang, Shujun Ou, Xiujie Liu, Shouyun Cao, Hongning Tong, Yonghong Wang, Feng Zhou, Hong Liao, Bin Hu, Chengcai Chu <<<

The intensive application of inorganic nitrogen underlies marked increases in crop production, but imposes detrimental effects on ecosystems: it is therefore crucial for future sustainable agriculture to improve the nitrogen-use efficiency of crop plants. Here we report the genetic basis of nitrogen-use efficiency associated with adaptation to local soils in rice (Oryza sativa L.). Using a panel of diverse rice germplasm collected from different ecogeographical regions, we performed a genome-wide association study on the tillering response to nitrogen-the trait that is most closely correlated with nitrogen-use efficiency in rice-and identified OsTCP19 as a modulator of this tillering response through its transcriptional response to nitrogen and its targeting to the tiller-promoting gene DWARF AND LOW-TILLERING (DLT). A 29-bp insertion and/or deletion in the OsTCP19 promoter confers a differential transcriptional response and variation in the tillering response to nitrogen among rice varieties. The allele of OsTCP19 associated with a high tillering response to nitrogen is prevalent in wild rice populations, but has largely been lost in modern cultivars: this loss correlates with increased local soil nitrogen content, which suggests that it might have contributed to geographical adaptation in rice. Introgression of the allele associated with a high tillering response into modern rice cultivars boosts grain yield and nitrogen-use efficiency under low or moderate levels of nitrogen, which demonstrates substantial potential for rice breeding and the amelioration of negative environment effects by reducing the application of nitrogen to crops. <<<