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The prevalence of deleterious mutations during the domestication and improvement of soybean

The Crop Journal 2023年第2期11卷 523-530页

作者： Shichao Sun Yumin Wang He Wei David E.Hufnagel Ya Wang Shiyu Guo Yinghui Li Li Wang Li-juan Qiu Shenzhen Branch Guangdong Laboratory for Lingnan Modern Agriculture/Genome Analysis Laboratory of the Ministry of Agriculture/Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural SciencesShenzhen 518000GuangdongChina Soybean Research Institute Jilin Academy of Agricultural SciencesChangchun 130033JilinChina Henan Academy of Crops Molecular Breeding Henan Academy of Agricultural Sciences/National Centre for Plant BreedingZhengzhou 450002HenanChina Virus and Prion Research Unit National Animal Disease CenterThe Agricultural Research Service(ARS)of the United States Department of Agriculture(USDA)AmesIA 50010USA The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement(MOA)/Key Laboratory of Soybean Biology(Beijing)(MOA) Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Kunpeng Institute of Modern Agriculture at Foshan Foshan 528200GuangdongChina

Soybean(Glycine max L.)is a protein and oil crop grown worldwide.Its fitness may be reduced by deleterious mutations,whose identification and purging is desirable for crop breeding.In the published whole-genome re-sequenced data of 2214 soybean accessions,including 221 wild soybean,1132 landrace cultivars and 861 improved soybean lines,we identified 115,275 deleterious single-nucleotide polymorphisms(SNPs).Numbers of deleterious alleles increased from wild soybeans to landraces and decreased from landraces to modern improved lines.Genes in selective-sweep regions showed fewer deleterious mutations than the remaining genes.deleterious mutations explained 4.3%-48%more phenotypic variation than randomly selected SNPs for resistance to soybean cyst nematode race 2(SCN2),soybean cyst nematode race 3(SCN3)and soybean mosaic virus race 3(SMV3).These findings illustrate how mutation load has shifted during soybean domestication,expansion and improvement and provide candidate sites for breeding out deleterious mutations in soybean by genome editing and/or conventional breeding focused on the selection of progeny with fewer deleterious alleles.

关键词： deleterious mutations Domestication cost Expansion load BAD_mutations Soybean cyst nematode

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Conservation genomic investigation of an endangered conifer,Thuja sutchuenensis,reveals low genetic diversity but also low genetic load

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Plant Diversity 2024年第1期46卷 78-90页

作者： Tongzhou Tao Richard IMilne Jialiang Li Heng Yang Shiyang Wang Sihan Chen Kangshan Mao Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education&Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station College of Life ScienceSichuan UniversityChengduChina Institute of Molecular Plant Science School of Biological ScienceUniversity of EdinburghEdinburgh EH93BFUK College of Science Tibet UniversityLhasa 850000Xizang Autonomous RegionPR China

Endangered species generally have small populations with low genetic diversity and a high genetic load.Thuja sutchuenensis is an endangered conifer endemic to southwestern China.It was once considered extinct in the wild,but in 1999 was rediscovered.However,little is known about its genetic load.We collected 67 individuals from five wild,isolated T.sutchuenensis populations,and used 636,151 SNPs to analyze the level of genetic diversity and genetic load in T.sutchuenensis to delineate the conservation units of T.sutchuenensis,based on whole transcriptome sequencing data,as well as target capture sequencing data.We found that populations of T.sutchuenensis could be divided into three groups.These groups had low levels genetic diversity and were moderately genetically differentiated.Our findings also indicate that T.sutchuenensis suffered two severe bottlenecks around the Last Glaciation Period and Last Glacial Maximum.Among Thuja species,T.sutchuenensis presented the lowest genetic load and hence might have purged deleterious mutations efficiently through purifying selection.However,distribution of fitness effects analysis indicated a high extinction risk for T.sutchuenensis.Multiple lines of evidence identified three management units for T.sutchuenensis.Although T.sutchuenensis possesses a low genetic load,low genetic diversity,suboptimal fitness,and anthropogenic pressures all present an extinction risk for this rare conifer.This might also hold true for many endangered plant species in the mountains all over the world.

关键词： Sichuan Arborvitae Genetic load deleterious mutations Demographic history Conservation genomics

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Mating behavior as an indicator of quality of Drosophila subobscura males？

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Insect Science 2017年第1期24卷 122-132页

作者： Marija Savic Veselinovic Sofija Pavkovic-Lucic Zorana Kurbalija Novicic Mihailo Jelic Marina Stamenkovic-Radak Marko Andjelkovic Faculty of Biology University of Belgrade Belgrade Serbia Institute for Biological Research 'Sinisa Stankovic' University of Belgrade Belgrade Serbia Serbian Academy of Sciences and Arts Belgrade Serbia

According to current theoretical predictions, any deleterious mutations that reduce nonsexual fitness may have a negative influence on mating success. This means that sexual selection may remove deleterious mutations from the populations. Males of good genetic quality should be more successful in mating, compared to the males of lower genetic quality. As mating success is a condition dependent trait, large fractions of the genome may be a target of sexual selection and many behavioral traits are likely to be condition dependent. We manipulated the genetic quality of Drosophila subobscura males by inducing mutations with ionizing radiation and observed the effects of the obtained heterozygous mutations on male mating behavior： courtship occurrence, courtship latency, mating occurrence, latency to mating and duration of mating. We found possible effects of mutations. Females mated more frequently with male progeny of nonirradiated males and that these males courted females faster compared to the male progeny of irradiated males. Our findings indicate a possible important role of sexual selection in purging deleterious mutations.

关键词： condition dependence deleterious mutations female preference inbred lines ionizing radiation mutational load

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