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An Expanded View of Complex traits:From Polygenic to Omnigenic

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四川生理科学杂志 2024年第1期46卷 139-139页

作者： Evan A Boyle Department of Genetics Stanford University Stanford CA 94305 USA. Electronic address: eaboyle@stanford.edu. Department of Genetics Stanford University Stanford CA 94305 USA. Electronic address: yangili@stanford.edu. Department of Genetics Stanford University Stanford CA 94305 USA Department of Biology Stanford University Stanford CA 94305 USA Howard Hughes Medical Institute Stanford University Stanford CA 94305 USA. Electronic address: pritch@stanford.edu.

A central goal of genetics is to understand the links between genetic variation and disease.Intuitively,one might expect diseasecausing variants to cluster into key pathways that drive disease etiology.But for complex traits,association signals tend to be spread across most of the genome-including near many genes without an obvious connection to disease.

关键词： traits cluster Complex

Correction:Identification of SSR markers linked to the abscission of cotton boll traits and mining germplasm in Cotton

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Journal of Cotton Research 2024年第2期7卷 219-222页

作者： SHUI Guangling LIN Hairong MA Xiaomei ZHU Bo HAN Peng AINI Nurimanguli GUO Chunping WU Yuanlong PAN Zhenyuan YOU Chunyuan SONG Guoli NIE Xinhui Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan Agricultural CollegeShihezi UniversityShiheziXinjiang 832003China Cotton Institute Xinjiang Academy of Agriculture and Reclamation ScienceShiheziXinjiang 832000China Agricultural Science Research Institute of the 5 Division of Xinjiang Production and Construction CorpsShuangheXinjiang 833408China Modern Agricultural College Kashi UniversityKashiXinjiang 844000China National Key Laboratory of Crop Genetic Improvement College of Plant Sciences&TechnologyHuazhong Agricultural UniversityWuhanHubei 430070China National Key Laboratory of Cotton Bio‑Breeding and Integrated Utilization Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenan 455000China

Correction:J Cotton Res 7,20(2024)https://***/10.1186/s42397-024-00180-3 Following publication of the original article(Shui et al.2024),the author found 5 errors in the published article.1.One of the author’s name has been corrected from Gou Chunping to Guo Chunping.2.The reference(Zhao SQ.2016)in Table 2 has been updated to:Zhao SQ.Analysis on the major gene and multigene mixed inheritance and QTL mapping for early maturity traits in upland cotton.Chin Acad Agric Sci.***.https://***/10.3969/j.issn.201600501.(in Chinese with English abstract).3.In’Results’part,’Phenotype analysis of 238 cotton boll abscission among cotton accessions’paragraph,the phenotype analysis of AR1 ranging from 19.27%–63.79%,which was wrongly written as 19.27%-63.97%.4.The‘2018KRL’is modified to‘2018KEL’in Table 1.

关键词： germplasm traits cotton

Effects of Seeding Date and Density on Yield and Agronomic traits of Millet : A Case Study of Wangu 098 Variety of Millet

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Asian Agricultural Research 2024年第4期16卷 33-36页

作者： Yinting NIU Le JU Peiyu CHEN Zhigang YIN Xuejie QIANG Junxia LI Nanyang Academy of Sciences Nanyang 473000China Institute of Cereal Crops Henan Academy of Agricultural SciencesZhengzhou 450002China

[Objectives]To find out a suitable cultivation technique of Wangu 098 in Nanyang area,speed up the popularization,demonstration and application of Wangu 098,and provide a theoretical and practical basis for adjusting the planting structure and realizing the matching of improved varieties and methods.[Methods]The new self-bred millet variety Wangu 098 was used as the material,and the two-factor split zone experimental design was adopted.The effects of different sowing dates and densities on the yield,growth period and agronomic characters of millet were studied.[Results]The interaction of seeding date and density had a great effect on the yield and plant traits of millet.Millet yield was significantly and positively correlated with plant height,panicle length,single panicle weight,panicle grain weight and tiller number.[Conclusions]The reasonable combination of seeding date and density could give full play to the yield potential of millet.According to the experimental results and cultivation experience,the suitable seeding date of millet in Nanyang area is in the first and middle ten days of June,and the best density is about 750000 plants/ha.However,after June 30,the seeding millet did not tiller,so the density should be increased to more than 900000 plants/ha to obtain higher yield.In terms of cultivation and management,timely seeding,reasonable close planting,and coordination of vegetative growth and reproductive growth can make the plant tall and strong,panicle long and thick,and improve the yield of millet.

关键词： Wangu 098 millet Seeding date Density Agronomic traits Yield

Peptides: Opening the door

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Molecular Plant 2024年第1期17卷 8-10页

作者： Zongcheng Lin Ke Jin Noni Franklin-Tong National Key Laboratory for Germplasm Innovation&Utilization of Horticultural Crops College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhan 430070China Hubei Hongshan Laboratory Wuhan 430070China School of Biosciences College of Life and Environmental SciencesUniversity of BirminghamEdgbastonBirmingham B152TTUK

Interspecific isolation is a common mechanism adopted by plants to prevent gene flow between diverged species,thus maintaining species genetic integrity.However,from a plant breeder's perspective,hybridization is desirable,as it can provide a wider range of agriculturally important traits for crop improvement(Tonosaki et al.,2016).Although significant progress has been made in recent years in our understanding of some key factors controlling pollen-pistil interactions within species,we still know virtually nothing about the genetic and molecular basis underlying interspecific incompatibility.

关键词： traits breed nothing

Harnessing genetic variation at regulatory regions to fine-tune traits for climate-resilient crops

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Molecular Plant 2022年第2期15卷 222-224页

作者： Diep R.Ganguly Lee T.Hickey Peter A.Crisp Australian Research Council Centre of Excellence in Plant Energy Biology Research School of BiologyThe Australian National UniversityActonCanberraACT 2601Australia CSIRO Synthetic Biology Future Science Platform CanberraACTAustralia Queensland Alliance for Agriculture and Food Innovation The University of QueenslandBrisbaneQLD 4072Australia School of Agriculture and Food Sciences The University of QueenslandBrisbaneQLD 4072Australia

Climate change is making it more challenging to meet the food demands of a growing global population.Increased food produc-tion relies on continual crop improvements to generate higher and more stable yields,especially with increasingly unpredictable environments and less arable land.The improvement of traits that promote climate resilience and resource utilization,for example,greater photosynthetic capacity,increased nitrogen use efficiency,and optimized root and shoot architecture,repre-sents a promising avenue for engineering crops to yield more with less(Evans and Lawson,2020).A key challenge for crop engineering is optimizing performance in specific environments.

关键词： crops traits environments

BnVIR:bridging the genotype-phenotype gap to accelerate mining of candidate variations underlying agronomic traits in Brassica napus

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Molecular Plant 2022年第5期15卷 779-782页

作者： Zhiquan Yang Congyuan Liang LuLu Wei Shengbo Wang Feifan Yin Dongxu Liu Liang Guo Yongming Zhou Qing-Yong Yang National Key Laboratory of Crop Genetic Improvement College of InformaticsHuazhong Agricultural UniversityWuhan 430070China Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhan 430070China

Dear Editor,Genetic variations,which range from single nucleotide polymor-phisms(SNPs)and short insertion/deletions(InDels)to large-scale structural variations(SVs),are the basis of phenotypic diversity.Understanding the effect of genetic variations on traits is critical for uncovering the genetic architecture of various phe-notypes.

关键词： agronomic traits InDel

Two haplotype-resolved genomes reveal important flower traits in bigleaf hydrangea(Hydrangea macrophylla)and insights into Asterid evolution

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Horticulture Research 2023年第12期10卷 45-57页

作者： Xingbo Wu Sheron A.Simpson Ramey C.Youngblood Xiaofen FLiu Brian E.Scheffler Timothy A.Rinehart Lisa W.Alexander Amanda M.Hulse-Kemp Department of Environmental Horticulture Tropical Research and Education CenterUniversity of FloridaHomesteadFL 33031United States Genomics and Bioinformatics Research Unit USDA-ARSRaleighNC 27695United States Genomics and Bioinformatics Research Unit USDA-ARSStonevilleMS 38776United States Institute for Genomics Biocomputing and BiotechnologyMississippi State UniversityStarkvilleMS 39762United States Crop Production and Protection USDA-ARSBeltsvilleMD 20705United States Floral and Nursery Plants Research Unit U.S.National ArboretumUSDA-ARSMcMinnvilleTN 37110United States Department of Crop and Soil Sciences North Carolina State UniversityRaleighNC 27695United States

The Hydrangea genus belongs to the Hydrangeaceae family,in the Cornales order of flowering plants,which early diverged among the Asterids,and includes several species that are commonly used ornamental plants.Of them,Hydrangea macrophylla is one of the most valuable species in the nursery trade,yet few genomic resources are available for this crop or closely related Asterid species.Two high-quality haplotype-resolved reference genomes of hydrangea cultivars‘Veitchii’and‘Endless Summer’[highest quality at 2.22 gigabase pairs(Gb),396 contigs,N5022.8 megabase pairs(Mb)]were assembled and scaffolded into the expected 18 pseudochromosomes.Utilizing the newly developed high-quality reference genomes along with high-quality genomes of other related flowering plants,nuclear data were found to support a single divergence point in the Asterids clade where both the Cornales and Ericales diverged from the euasterids.Genetic mapping with an F1 hybrid population demonstrated the power of linkage mapping combined with the new genomic resources to identify the gene for inflorescence shape,CYP78A5 located on chromosome 4,and a novel gene,BAM3 located on chromosome 17,for causing double flower.Resources developed in this study will not only help to accelerate hydrangea genetic improvement but also contribute to understanding the largest group of flowering plants,the Asterids.

关键词： Hydra traits resolved

Genome-wide association analysis identified molecular markers and candidate genes for flower traits in Chinese orchid (Cymbidium sinense)

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Horticulture Research 2023年第11期10卷 193-207页

作者： Fengxi Yang Yudi Guo Jie Li Chuqiao Lu Yonglu Wei Jie Gao Qi Xie Jianpeng Jin Genfa Zhu Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization Environmental Horticulture Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou 510640China

The orchid,the champagne of f lowers,brings luxury,elegance,and novelty to nature.Cymbidium sinense is a symbol of gigantic floral variability on account ofwavering shapes and sizes of f loral organs,althoughmarker-trait association(MTA)has not been studied for its f loral traits.We evaluated markers associated with 14 f loral traits of C.sinense through a genome-wide association study(GWAS)of 195 accessions.A total of 65318522 single-nucleotide polymorphisms(SNPs)and 3906176 insertion/deletion(InDel)events were identified through genotyping-by-sequencing.Among these,4694 potential SNPs and 477 InDelswere identified as MTAs at−log10 P>5.The genes related to these SNPs and InDels were largely associated with f loral regulators,hormonal pathways,cell division,and metabolism,playing essential roles in tailoring f loral morphology.Moreover,20 candidate SNPs/InDels linked to 11 genes were verified,8 of which were situated on exons,onewas located in the 5-UTR and twowere positioned in introns.Here,themultitepal trait-related gene RABBIT EARS(RBE)was found to be the most crucial gene.We analyzed the role of CsRBE in the regulation of flower-related genes via efficient transient overexpression in C.sinense protoplasts,and found that the floral homeotic genes CsAP3 and CsPI,as well as organ boundary regulators,including CsCUC and CsTCP genes,were regulated by CsRBE.Thus,we obtained key gene loci for important ornamental traits of orchids using genome-wide association analysis of populations with natural variation.The findings of this study can do a great deal to expedite orchid breeding programs for shape variability.

关键词： traits analysis breeding

Genome-wide association study of 23 f lowering phenology traits and 4 f loral agronomic traits in tree peony (Paeonia section Moutan DC.) reveals five genes known to regulate f lowering time

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Horticulture Research 2023年第2期10卷 118-133页

作者： Yuying Li Lili Guo Zhanying Wang Dehui Zhao Dalong Guo John E.Carlson Weilun Yin Xiaogai Hou College of Agronomy/College of Tree Peony Henan University of Science and TechnologyLuoyangHenan471023China Luoyang Academy of Agricultural and Forestry Sciences LuoyangHenan471000China College of Forestry Henan University of Science and TechnologyLuoyangHenan471023China Department of Ecosystem Science and Management Pennsylvania State UniversityUniversity ParkPA 16802USA College of Biological Sciences and Technology Beijing Forestry UniversityBeijing 100083China

Tree peony is a unique traditional f lower in China,with large,fragrant,and colorful f lowers.However,a relatively short and concentrated f lowering period limits the applications and production of tree peony.A genome-wide association study(GWAS)was conducted to accelerate molecular breeding for the improvement of f lowering phenology traits and ornamental phenotypes in tree peony.A diverse panel of 451 tree peony accessions was phenotyped for 23 f lowering phenology traits and 4 f loral agronomic traits over 3 years.Genotyping by sequencing(GBS)was used to obtain a large number of genome-wide single-nucleotide polymorphisms(SNPs)(107050)for the panel genotypes,and 1047 candidate genes were identified by association mapping.Eighty-two related genes were observed during at least 2 years for f lowering,and seven SNPs repeatedly identified for multiple f lowering phenology traits over multiple years were highly significantly associated with five genes known to regulate f lowering time.We validated the temporal expression profiles of these candidate genes and highlighted their possible roles in the regulation of f lower bud differentiation and f lowering time in tree peony.This study shows that GWAS based on GBS can be used to identify the genetic determinants of complex traits in tree peony.The results expand our understanding of f lowering time control in perennial woody plants.Identification of markers closely related to these f lowering phenology traits can be used in tree peony breeding programs for important agronomic traits.

关键词： breeding traits tree