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

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.

Multiomics comparison among populations of three plant sources of Amomi Fructus

Amomi Fructus(Sharen,AF)is a traditional Chinese medicine(TCM)from three source species(or varieties),including Wurfbainia villosa var.villosa(WVV),W.villosa var.xanthioides(WVX),or W.longiligularis(WL).Among them,WVV has been transplanted from its top-geoherb region,Guangdong,to its current main production area,Yunnan,for>50 years in China.However,the genetic and transcriptomic differentiation among multiple AF source species(or varieties)and between the origin and transplanted populations of WVV is unknown.In our study,the observed overall higher expression of terpenoid biosynthesis genes in WVV than in WVX provided possible evidence for the better pharmacological effect of WVV.We also screened six candidate borneol dehydrogenases(BDHs)that potentially catalyzed borneol into camphor in WVV and functionally verified them.Highly expressed genes at the P2 stage of WVV,Wv05G1424 and Wv05G1438,were capable of catalyzing the formation of camphor from(+)-borneol,(-)-borneol and DL-isoborneol.Moreover,the BDH genes may experience independent evolution after acquiring the ancestral copies,and the following tandem duplications might account for the abundant camphor content in WVV.Furthermore,four populations of WVV,WVX,and WL are genetically differentiated,and the gene flow from WVX to WVV in Yunnan contributed to the greater genetic diversity in the introduced population(WVV-JH)than in its top-geoherb region(WVV-YC),which showed the lowest genetic diversity and might undergo genetic degradation.In addition,terpene synthesis(TPS)and BDH genes were selected among populations of multiple AF source species(or varieties)and between the top-and non-top-geoherb regions,which might explain the difference in metabolites between these populations.Our findings provide important guidance for the conservation,genetic improvement,and industrial development of the three source species(or varieties)and for identifying top-geoherbalism with molecular markers,and proper clinical application of AF.

The cotton WRKY transcription factor GhWRKY70 negatively regulates the defense response against Verticillium dahliae

WRKY transcription factors (TFs) play important roles in the regulation of biotic and abiotic stresses. However, the functions of most WRKY TFs in upland cotton (Gossypium hirsutum) are still unknown. In this study, we functionally identified a group Ⅲ WRKY transcription factor, GhWRKY70, in upland cotton. Reverse transcription-quantitative PCR analysis showed that GhWRKY70 expression was induced by Verticillium dahliae, salicylic acid (SA) and methyl jasmonate. Virus-induced gene silencing of GhWRKY70 increased the resistance of cotton to V. dahliae. Specifically, jasmonic acid (JA) response-associated genes were upregulated and SA-related genes were downregulated in GhWRKY70-silenced cotton plants. Overexpression of GhWRKY70 reduced tolerance to V. dahliae in Arabidopsis thaliana. Transgenic Arabidopsis plants showed increased expression of SA-associated genes and reduced expression of JA response-associated genes. These results suggest that GhWRKY70 negatively regulates tolerance to V. dahliae in at least two ways: (ⅰ) by upregulating the expression of SA-associated genes and (ⅱ) by reducing the expression of JA-associated genes.