Single-nucleus RNA and ATAC sequencing analyses provide molecular insights into early pod development of peanut fruit

Peanut(Arachis hypogaea L.)is an important leguminous oil and economic crop that produces flowers aboveground and fruits belowground.Subterranean fruit-pod development,which significantly affects peanut production,involves complex molecular mechanisms that likely require the coordinated regulation of multiple genes in different tissues.To investigate the molecular mechanisms that underlie peanut fruitpod development,we characterized the anatomical features of early fruit-pod development and integrated single-nucleus RNA-sequencing(snRNA-seq)and single-nucleus assay for transposase-accessible chromatin with sequencing(snATAC-seq)data at the single-cell level.We identified distinct cell types,such as meristem,embryo,vascular tissue,cuticular layer,and stele cells within the shell wall.These specific cell types were used to examine potential molecular changes unique to each cell type during pivotal stages of fruit-pod development.snRNA-seq analyses of differentially expressed genes revealed cell-type-specific insights that were not previously obtainable from transcriptome analyses of bulk RNA.For instance,we identified MADS-box genes that contributes to the formation of parenchyma cells and gravity-related genes that are present in the vascular cells,indicating an essential role for the vascular cells in peg gravitropism.Overall,our single-nucleus analysis provides comprehensive and novel information on specific cell types,gene expression,and chromatin accessibility during the early stages of fruit-pod development.This information will enhance our understanding of the mechanisms that underlie fruit-pod development in peanut and contribute to efforts aimed at improving peanut production.

Genomic analysis of sugar transporter genes in peanut (Arachis hypogaea):Characteristic,evolution and expression profiles during development and stress

Peanut(Arachis hypogaea L.) is an economically significant crop with aerial cleistogamous flowers and subterranean geocarpic fruit(pods).The formation of peanut pod requires movement of the embryo from air to ground and then development in the soil,which is a complex biological process involving transport and accumulation of sugars.Sugar transport proteins(STP) mediate the transport of monosaccharides in various physiological processes,including fertilization,ovary formation,and seed development.In this study,a total of 36 AhSTP genes(AhSTP1–36) containing the conserved sugar_tr motif were identified in the A.hypogaea genome.Phylogenetic analysis revealed that AhSTP genes were classified into four clades,and the arrangement of motifs in AhSTP proteins was similar within clades.Synteny analysis revealed that segmental duplication events have played an important role in the expansion of STP genes in peanut,and chromosome rearrangements might have facilitated the exchange of STP genes between the A and B sub-genomes.Transcriptome analyses revealed that the expression patterns of AhSTP genes varied among tissues.Hormone and abiotic stress treatments could upregulate or down-regulate the expression of AhSTP genes,and low temperature had a major effect on the expression of most AhSTP genes.Four AhSTP genes(AhSTP3,AhSTP9,AhSTP19,and AhSTP28) were specifically expressed in the pod,indicating that these genes might be involved in pod formation and development in peanut.The unique expression of these four genes during pod construction and development was confirmed in two different type cultivars using quantitative real-time PCR analysis.Our findings provide new insights into the STP gene family in peanut and will aid future functional studies of AhSTP genes.

菜用大豆荚粒品质发育过程及适宜采摘期分析

选用夏播菜用大豆不同熟期组 6个代表品种通州豆、楚秀 (熟期组Ⅲ ) ,海系 13、南农 87c -38(熟期组Ⅳ ) ,南农大黄豆、黑皮绿仁 (熟期组Ⅴ ) ,对其荚粒品质发育过程进行系统观察。结果表明 :(1)荚长、荚宽及荚厚的发育符合Logistic生长曲线 ,荚长、荚宽在开花后 10 - 2 0天伸长较快 ,基本接近品种的固有长度和宽度 ;荚厚在开花后 2 5 - 40天快速增长。 (2 )百荚鲜重、百粒鲜重发育符合二次曲线 ,熟期组Ⅲ品种在开花后 35 - 5 5天达到最大值 ,而熟期组Ⅳ、熟期组Ⅴ品种在开花后5 5 - 70天达到最大值。 (3)出籽率及可溶性糖的变化符合四次曲线方程 ,在R5-R7前半期可溶性糖含量逐渐提高 ,R7后半期有所回落 ;不同熟期组的菜用大豆生长发育变化相似。菜用大豆的适宜采摘期为R6 -R7的前半期。

甘蓝型油菜不同发育时期角果重量的遗传分析

采用可以估算不同发育时期基因累加效应和特定发育时期净遗传效应的遗传模型和统计分析方法,研究油菜角果成熟过程中其重量的发育遗传规律.结果表明,控制不同发育时期油菜角果重量表现的基因累加效应以加性效应为主,仅在第22d时其显性效应大于加性效应.条件分析的结果表明,控制角果重量的基因在角果多数发育时期中均有新的表达,且其表达方式有所不同,其中角果重量的净遗传效应表达量以开花后第16～22d最大.角果重量在不同发育时刻具有较高的狭义遗传率,低世代选择可以取得良好的育种效果.亲本遗传效应分析表明,双20-4、中R-888和Tower3个亲本有利于增加杂种后代的角果重量,其中以中R-888最优.杂种优势分析表明,角果发育的前中期(16～29d)群体平均优势明显大于其他发育时期.

Identification of genomic regions determining flower and pod numbers development in soybean (Glycine max L.)

Flower and pod numbers per plant are important agronomic traits underlying soybean yield. So far quantitative trait loci （QTL） de- tected for flower and pod-related traits have mainly focused on the final stage, and might therefore have ignored genetic effects expressed during a specific developmental stage. Here, dynamic expressions of QTL for flower and pod numbers were identified using 152 recom- binant inbred lines （RILs） and a linkage map of 306 markers. Wide genetic variation was found among RILs; 17 unconditional and 18 conditional QTL were detected for the two traits at different developmental stages over two years. Some QTL were detected only at one stage and others across two or more stages, indicating that soybean flower and pod numbers development may be governed by time-dependent gene expression. Three main QTL （qfn-Chrl8-2, qfn-Chr20-1, and qfn-Chr19） were detected for flower number, and two main QTL （qpn-Chrll and qpn-Chr20） were detected for pod number. The phenotypic variation explained by them ranged from 6.1% to 34.7%. The markers linked to these QTL could be used in marker-assisted selection for increasing soybean flower and pod numbers, with the ultimate aim of increasing soybean yield. Comparison of the QTL regions for flower and pod numbers traits with the related genes reported previously showed that seven and four related genes were located in the QTL regions of qfn-Chr11 and qfn-Chr19, respectively. These results provide a basis for free mapping and cloning of flower and pod development-related genes.

绿豆荚果发育及籽粒灌浆特性

为探明绿豆开花后荚粒生长发育规律及籽粒灌浆和物质积累特性,以‘西绿1号’和‘安绿7号’绿豆品种为试验材料,对开花后绿豆荚色、粒色、荚长、荚宽、荚体积、籽粒体积、荚粒数、荚壳鲜重、荚壳干重、百荚鲜重、百荚干重、百粒鲜重和百粒干重等性状的变化进行测定,分析绿豆荚果发育过程中荚壳和籽粒干物质分配以及籽粒灌浆速率变化,用Logistic方程拟合灌浆过程,并进行相关性分析。结果表明:绿豆籽粒形成过程中,荚色从深绿色转为绿色再转为黑色,粒色从透亮青绿色到嫩绿色再到深绿色;荚长和荚宽为先增长后基本保持平稳的趋势,荚体积和籽粒体积的变化趋势均为先增长后下降再趋于平缓;籽粒含水量呈不断下降趋势,荚壳干物质分配指数不断降低,籽粒干物质分配指数不断增大,籽粒灌浆速率呈慢-快-慢的单峰曲线变化,在开花后15d左右达到峰值,灌浆过程符合Logistic方程。相关性分析表明,绿豆百粒干重与百荚干重呈极显著正相关,百粒鲜重与籽粒体积呈极显著正相关,与荚宽、荚体积、荚壳干重呈显著正相关,与荚粒数呈显著负相关;百粒干重与最大灌浆速率呈极显著负相关,与平均灌浆速率呈显著负相关,与生长活跃期呈极显著正相关。因此,绿豆育种中应选育大荚品种,栽培中注重花后15d前后的肥水供应,以保证籽粒灌浆饱满,实现高产优质。