Genetic dissection of yield-related traits in response to drought stress in common bean

Drought stress severely impairs common bean production.For facilitating drought-resistance breeding in common bean,molecular markers were identified in a genome-wide level marker–trait association study.A panel of 210 common bean accessions showed large variation in 11 agronomic traits at the adult stage(plant height,pod number per plant,seed number per pod,seed number per plant,seed yield per plant,pod length,harvest index,pod harvest index,days to maturity,hundred-seed weight,and seed yield)under two water conditions.The coefficient of variation ranged from 6.21% for pod harvest index to51.00% for seed number per plant under well-watered conditions,and from 4.05% for days to maturity to 40.72% for seed number per plant under drought stress.In a genome-wide association study,119quantitative-trait loci were associated with drought resistance,including 41 adjacent to known loci.Among these loci,12 were found to be associated with at least two traits.Three major loci were identified at Pv01 and Pv02.A set of candidate genes were found that encode MYBs,AREBs,WKRYs,and protein kinases.These results reveal promising alleles that control drought resistance,shedding light on the genetic basis of drought resistance and accelerating future efforts for drought resistance improvement in common bean.

Chromosome-level genome assembly of Salvia miltiorrhiza with orange roots uncovers the role of Sm2OGD3 in catalyzing 15,16-dehydrogenation of tanshinones

Salvia miltiorrhiza is well known for its clinical practice in treating heart and cardiovascular diseases.Its roots,used for traditional Chinese medicine materials,are usually brick-red due to accumulation of red pigments,such as tanshinone IIA and tanshinone I.Here we report a S.miltiorrhiza line(shh)with orange roots.Compared with the red roots of normal S.miltiorrhiza plants,the contents of tanshinones with a single bond at C-15,16 were increased,whereas those with a double bond at C-15,16 were significantly decreased in shh.We assembled a high-quality chromosome-level genome of shh.Phylogenomic analysis showed that the relationship between two S.miltiorrhiza lines with red roots was closer than the relationship with shh.It indicates that shh could not be the mutant of an extant S.miltiorrhiza line with red roots.Comparative genomic and transcriptomic analyses showed that a 1.0 kb DNA fragment was deleted in shh Sm2OGD3m.Complementation assay showed that overexpression of intact Sm2OGD3 in shh hairy roots recovered furan D-ring tanshinone accumulation.Consistently,in vitro protein assay showed that Sm2OGD3 catalyzed the conversion of cyptotanshinone,15,16-dihydrotanshinone I and 1,2,15,16-tetrahydrotanshinone I into tanshinone IIA,tanshinone I and 1,2-dihydrotanshinone I,respectively.Thus,Sm2OGD3 functions as tanshinone 15,16-dehydrogenase and is a key enzyme in tanshinone biosynthesis.The results provide novel insights into the metabolic network of medicinally important tanshinone compounds.

普通菜豆抗菜豆象性状的全基因组关联分析

普通菜豆(Phaseolus vulgaris)具有丰富的营养价值,菜豆象(Acanthoscelides obtectus)是危害菜豆的主要害虫,利用抗虫种质资源防治菜豆象是最安全且经济有效的方法。该研究利用改良的室内人工接虫方法,对625份普通菜豆种质资源进行2次菜豆象抗性重复鉴定,筛选出2份抗性稳定且种子受害率均在10%以下的高抗种质。利用种子受害率和蛀孔总数的表型数据,基于3767432个SNP标记进行全基因组关联分析,鉴定出15个与种子受害率相关的显著关联遗传位点,8个与蛀孔总数相关的显著关联位点,解释了4.54%–5.56%的表型变异。在候选位点筛选出包括编码蛋白酶抑制剂、凝集素和过氧化物酶等在内的20个与抗虫防御相关的候选基因。

普通菜豆镰孢菌枯萎病抗性种质资源筛选及全基因组关联分析

普通菜豆镰孢菌枯萎病是严重制约菜豆(Phaseolus vulgaris)产量的主要病害之一。采用下胚轴双孔注射法对601份普通菜豆种质资源进行枯萎病抗性鉴定,共筛选出4份高抗材料。在此基础上,基于分布在全基因组上的3765456个单核苷酸多态性(SNP)标记,进行全基因组关联分析,以P<1×10^(–5)为阈值。结果检测到57个显著关联的SNP位点,分布于1、2、6、8和11号染色体上;共获得8个显著关联区域,其中位于1号染色体上的区域1包含SNP最多(48个),最显著SNP P值为2.18E–07。在8个显著关联区域中,共检测到186个基因,其中157个基因有注释信息,编码过氧化物酶、抗病蛋白、转录因子和蛋白激酶等。结合KEGG富集分析和序列同源性比对,鉴定出9个候选基因可能与抗性相关。