QTL analysis for plant height and fine mapping of two environmentally stable QTLs with major effects in soybean

Plant height is an important agronomic trait, which is governed by multiple genes with major or minor effects. Of numerous QTLs for plant height reported in soybean, most are in large genomic regions, which results in a still unknown molecular mechanism for plant height. Increasing the density of molecular markers in genetic maps will significantly improve the efficiency and accuracy of QTL mapping. This study constructed a high-density genetic map using 4 011 recombination bin markers developed from whole genome re-sequencing of 241 recombinant inbred lines(RILs) and their bi-parents, Zhonghuang 13(ZH) and Zhongpin 03-5373(ZP). The total genetic distance of this bin map was 3 139.15 cM,with an average interval of 0.78 cM between adjacent bin markers. Comparative genomic analysis indicated that this genetic map showed a high collinearity with the soybean reference genome. Based on this bin map, nine QTLs for plant height were detected across six environments, including three novel loci(qPH-b_11, qPH-b_17 and qPH-b_18). Of them, two environmentally stable QTLs qPH-b_13 and qPH-b_19-1 played a major role in plant height, which explained 10.56-32.7% of the phenotypic variance. They were fine-mapped to 440.12 and 237.06 kb region, covering 54 and 28 annotated genes, respectively. Via the function of homologous genes in Arabidopsis and expression analysis, two genes of them were preferentially predicted as candidate genes for further study.

Identification and characterization of long-InDels through whole genome resequencing to facilitate fine-mapping of a QTL for plant height in soybean(Glycine max L.Merr.)

With the development of sequencing technology, insertions-deletions(InDels) have been increasingly reported to be involved in the genetic determination of agronomical traits. However, most studies have focused on the identification and application of short-InDels(1–15 bp) for genetic analysis. The objective of this study was to deeply deploy long-InDels(>15 bp) for the genetic analysis of important agronomic traits in soybean. A total of 13 573 polymorphic long-InDels were identified between parents Zhongpin 03-5373(ZP) and Zhonghuang 13(ZH), which were unevenly distributed on 20 chromosomes of soybean, varying from 321 in Chr11 to 1 246 in Chr18. Consistent with the distribution pattern of annotated genes, the average density of long-InDels in arm regions was significantly higher than that in pericentromeric regions at the P=0.01 level. A total of 2 704(19.9% of total) long-InDels were located in genic regions, including 319 large-effect long-InDels, which resulted in truncated or elongated protein sequences. A previously identified QTL(qP H16) underlying plant height was further analyzed, and it was found that 26 out of 35(74.3%) long-InDel markers located in the qPH16 region showed clear polymorphisms between parents ZP and ZH. Seven markers, including three long-InDels and four previously reported SNP markers, were used to genotype 242 recombinant inbred lines derived from ZP×ZH. As a result, the qPH16 locus was narrowed from a 960-kb region to a 477.55-kb region, containing 65 annotated genes. Therefore, these long-InDels are a complementary genetic resource of SNPs and short-InDels for plant height and can facilitate genetic studies and molecular assisted selection breeding in soybean.

Establishment and application of an accurate identification method for fragrant soybeans

In order to screen the aroma characteristics of soybean,a new method was established which can quickly quantify the content of 2-acetyl-1pyrroline(2-AP),an important compound related to soybean aroma,using gas chromatography-mass spectrometry(GC-MS).Based on peak profile,total peak area and retention time as test indexes,an accurate identification method for fragrant soybeans was established.The optimum parameters of the protocol consisted of column temperature70℃,sample injector temperature 180℃,optimum extraction alcohol content 1 m L,Na Cl content 0.1 g,ultrasonication time10 min,and extraction time 1 h,which were established by using the orthogonal test of single factors and three factors with four levels(L_9(3)^4).2-AP content of leaves had significant correlations with seeds,which were easier to measure.The protocol was simple and easy to carry out,consumed only small amounts of reagents,and provided accurate and reliable results with good reproducibility.A total of 101 soybean genotypes from different geographical sources were analyzed using this protocol.The results showed that the average content of 2-AP was 0.29 mg L^(–1),ranging from 0.094 to 1.816 mg L^(–1),and the genetic diversity index was 0.54.Among all genotypes-tested,they were classified into three grades,including seven elite genotypes identified as"grade one fragrant soybeans",which were Zhonglong 608,Heinong 88,Ha13-2958,Hongmiandou,Heinong 82,Huangmaodou,and Jiyu 21.These results provide both an identification technique and several elite aroma genotypes for gene discovery and good quality breeding in soybean.

Differential Expression and Regulation of Switchgrass Root MicroRNA in Response to Alkali-salt Stress Using High-throughput Deep Sequencing

Switchgrass(Panicum virgatum L.)as a high-quality bioenergy crop that can effectively improve saline-alkali soil has strong resistance to stress and grows well in marginal soil and some abiotic stress environments.This study used alkali-sensitive genotype AM(AM-314/MS-155)and alkali-tolerant genotype ALA(Alamo)as experimental materials to investigate molecular mechanisms of switchgrass tolerance to alkali-salt stress.When the plants were grown to E5 stage,the alkali-salt stress treatment was carried out by soaking method(Na2CO3:NaHCO3=1:9,C(Na+)=150 mmol·L-1 and pH=9.0)and fresh root samples were taken after treatments for 0(CK),6 and 24 h,respectively,the differentially expressed microRNAs and their regulatory network were analyzed.A total of 1049 known miRNAs and 68 novel miRNAs were identified.Seventy-two differentially expressed miRNAs in ALA were more than three times higher than those in AM and 36.1%differentially expressed miRNAs was significantly down-regulated(p<0.05).Through analyses of differentially expressed miRNAs and their target genes,it was found that under alkali-salt stress,differentially expressed miRNAs in AM were mainly involved in the regulation of cellular ROS clearance,ethylene signal transduction,and root,leaf and flower development.MiRNAs in ALA were also involved in water transport,DNA methylation,response to high osmotic pressure,activation of stress-related genes and more complex responses to alkali-salt stress processes,but those in AM were not.ALA was significantly higher than AM in the number of microRNAs responding to alkali-salt stress and in the functional diversity of their regulatory target genes.

A Deep Reinforcement Learning-Based Technique for Optimal Power Allocation in Multiple Access Communications

Formany years,researchers have explored power allocation(PA)algorithms driven bymodels in wireless networks where multiple-user communications with interference are present.Nowadays,data-driven machine learning methods have become quite popular in analyzing wireless communication systems,which among them deep reinforcement learning(DRL)has a significant role in solving optimization issues under certain constraints.To this purpose,in this paper,we investigate the PA problem in a k-user multiple access channels(MAC),where k transmitters(e.g.,mobile users)aim to send an independent message to a common receiver(e.g.,base station)through wireless channels.To this end,we first train the deep Q network(DQN)with a deep Q learning(DQL)algorithm over the simulation environment,utilizing offline learning.Then,the DQN will be used with the real data in the online training method for the PA issue by maximizing the sumrate subjected to the source power.Finally,the simulation results indicate that our proposedDQNmethod provides better performance in terms of the sumrate compared with the available DQL training approaches such as fractional programming(FP)and weighted minimum mean squared error(WMMSE).Additionally,by considering different user densities,we show that our proposed DQN outperforms benchmark algorithms,thereby,a good generalization ability is verified over wireless multi-user communication systems.

QTL mapping of drought tolerance traits in soybean with SLAF sequencing

Drought stress is an important factor affecting soybean yield.Improving drought tolerance of soybean varieties can increase yield and yield stability when the stress occurs.Identifying QTL related to drought tolerance using molecular marker-assisted selection is able to facilitate the development of drought-tolerant soybean varieties.In this study,we used a high-yielding and drought-sensitive cultivar‘Zhonghuang 35’and a drought-tolerant cultivar‘Jindou 21’to establish F6:9 recombinant inbred lines.We constructed a highdensity genetic map using specific locus amplified fragment sequencing(SLAF-Seq)technology.The genetic map contained 8078 SLAF markers distributing across 20 soybean chromosomes with a total genetic distance of 3780.98 c M and an average genetic distance of0.59 c M between adjacent markers.Two treatments(irrigation and drought)were used in the field tests,the Additive-Inclusive Composite Interval Mapping(ICIM-ADD)was used to call QTL,and plant height and seed weight per plant were used as the indicators of drought tolerance.We identified a total of 23 QTL related to drought tolerance.Among them,seven QTL(q PH2,q PH6,q PH7,q PH17,q PH19-1,q PH19-2,and q PH19-3)on chromosomes 2,6,7,17,and 19 were related to plant height,and five QTL(q SWPP2,q SWPP6,q SWPP13,q SWPP17,and q SWPP19)on chromosomes 2,6,13,17,and 19 were related to seed weight and could be considered as the major QTL.In addition,three common QTL(q PH6/q SWPP6,q PH17/q SWPP17,and q PH19-3/q SWPP19)for both plant height and seed weight per plant were located in the same genomic regions on the same chromosomes.Three(q PH2,q PH17,and q PH19-2)and four novel QTL(q SWPP2,q SWPP13,q SWPP17,and q SWPP19)were identified for plant height and seed weight per plant,respectively.Two pairs of QTL(q PH2/q SWPP2 and q PH17/q SWPP17)were also common for both plant height and seed weight per plant.These QTL and closely linked SLAF markers could be used to accelerate breeding for drought tolerant cultivars via MAS.

Map-based cloning of a novel QTL qBN-1 influencing branch number in soybean[Glycine max(L.)Merr.]

Branch number(BN)is an important agronomic attribute related to the plant architecture,adaptability,and yield of soybean.To date,few studies ofBNhave been conducted to elucidate its genetic background.We aimed to localize genetic factors affecting BN using segregating populations derived fromthe high-branching cultivar‘Kennong24’(KN24)and the low-branching cultivar‘Kenfeng19’(KF19).Composite interval mapping analysis detected a QTL(qBN-1)on chromosome 6 between the SSR markers BARCSOYSSR_06_0993 and BARCSOYSSR_06_1070 using an F2 population.To fine-map qBN-1,a RIL population was developed and genotyped with 14 SSRmarkers located in the QTL region.qBN-1 was localized to a 115.67-kb interval flanked by markers BARCSOYSSR_06_1048 and BARCSOYSSR_06_1053.The QTL was further confirmed using backcross populations of size 1305(BC2F2 with KN24 as a recurrent parent)and 1712(BC3F2 with KF19 as a recurrent parent).The fine-mapping region of qBN-1 contained only two candidate genes,Glyma.06G208800 and Glyma.06G208900,whose expression patterns were investigated by qRT-PCR.Compared to Glyma.06G208800 gene expression,Glyma.06G208900 showed the highest expression of the two genes and showed a significant difference in expression between high-and low-branching genotypes in either axillary meristem or shoot apical meristem,and showed opposite expression patterns in the two tissues at V4 and R1 stages.These results identify Glyma.06G208900 as a novel candidate gene controlling BN.Taken together,the results of this study provide a foundation for cloning and functional analysis of the qBN-1 gene and for the improvement of BN bymarker-assisted selection in soybean breeding.

The genome of the warm-season turfgrass African bermudagrass (Cynodon transvaalensis)

Cynodon species can be used for multiple purposes and have high economic and ecological significance.However,the genetic basis of the favorable agronomic traits of Cynodon species is poorly understood,partially due to the limited availability of genomic resources.In this study,we report a chromosome-scale genome assembly of a diploid Cynodon species,C.transvaalensis,obtained by combining Illumina and Nanopore sequencing,BioNano,and Hi-C.The assembly contains 282 scaffolds(~423.42 Mb,N50=5.37 Mb),which cover~93.2%of the estimated genome of C.transvaalensis(~454.4Mb).Furthermore,90.48%of the scaffolds(~383.08 Mb)were anchored to nine pseudomolecules,of which the largest was 60.78Mb in length.Evolutionary analysis along with transcriptome comparison provided a preliminary genomic basis for the adaptation of this species to tropical and/or subtropical climates,typically with dry summers.The genomic resources generated in this study will not only facilitate evolutionary studies of the Chloridoideae subfamily,in particular,the Cynodonteae tribe,but also facilitate functional genomic research and genetic breeding in Cynodon species for new leading turfgrass cultivars in the future.

Combining Agronomic and Pest Studies to Identify Vegetable Soybean Genotypes Suitable for Commercial Edamame Production in the Mid-Atlantic U.S.

Currently, domestic production of vegetable soybean (aka “edamame”) lags well behind consumer demand, with approximately 70% of U.S.-consumed edamame imported each year. A major barrier for growth of the U.S. edamame industry is an overall lack of varieties with adequate consumer acceptability and adaption to the U.S. climate and environment. In this study, we evaluated eleven vegetable soybean genotypes (including one commercial check) for differences in yield, pod size, and resistance to local insect, bacterial, and fungal pressures in order to identify genotypes with the greatest potential for use in commercial edamame production. Although there were variations in average pod length (42.1 - 53.6 mm), width (10.9 - 12.7 mm), and thickness (6.29 - 7.34 mm) among the genotypes, only pod length showed statistical significance. In addition, genotype significantly affected fresh pod yield. The prevalence of specific insect pests varied by location and year and included soybean aphid, potato leafhopper, Mexican bean beetle, as well as a complex of stink bugs and lepidopteran larvae. For each of these insect pests, significant differences were observed. Some plant diseases observed on the edamame genotypes included: downy mildew, bacterial pustule, Fusarium pod rot, Cercospora blight and purple seed stain, and damping off. In 2018, in Whitethorne, VA, soybean downy mildew was quite prevalent and disease symptoms varied considerably. Overall, genotypes V16-0524 and R15-10280 showed particularly favorable yield, and resilience to native pests compared to the commercial check, UA-Kirksey. The genotypes V16-0524 and R15-10280 showed strong potential to increase the availability of varieties that can be used for commercial edamame production in the Mid-Atlantic region.

Engineered Cleistogamy in Camelina sativa for bioconfinement

Camelina sativa is a self-pollinating and facultative outcrossing oilseed crop.Genetic engineering has been used to improve camelina yield potential for altered fatty acid composition,modified protein profiles,improved seed and oil yield,and enhanced drought resistance.The deployment of transgenic camelina in the field posits high risks related to the introgression of transgenes into nontransgenic camelina and wild relatives.Thus,effective bioconfinement strategies need to be developed to prevent pollen-mediated gene f low(PMGF)from transgenic camelina.In the present study,we overexpressed the cleistogamy(i.e.f loral petal non-openness)-inducing PpJAZ1 gene from peach in transgenic camelina.Transgenic camelina overexpressing PpJAZ1 showed three levels of cleistogamy,affected pollen germination rates after anthesis but not during anthesis,and caused a minor silicle abortion only on the main branches.We also conducted field trials to examine the effects of the overexpressed PpJAZ1 on PMGF in the field,and found that the overexpressed PpJAZ1 dramatically inhibited PMGF from transgenic camelina to non-transgenic camelina under the field conditions.Thus,the engineered cleistogamy using the overexpressed PpJAZ1 is a highly effective bioconfinement strategy to limit PMGF from transgenic camelina,and could be used for bioconfinement in other dicot species.

Climate drives differences in the germination niche of a globally distributed invasive grass

外来入侵物种在入侵地经常面临很强的选择压力,这常常导致种内变异。在生活史事件发生的时间上,种群分化对气候梯度的响应被认为是促进许多入侵物种扩张的重要机制。对于产生种子的植物来说,种子萌发的时间决定了萌芽所经历的第一个环境条件,这对入侵植物的成功定植、种群建立和传播具有重要意义——尽管对于萌发在植物入侵成功中所起的作用仍然知之甚少。在本研究中,我们评估了入侵植物石茅(Sorghum halepense)在北美分布的10个种群的种子萌发在温度和降水梯度上的动态变化,以及这种变化是否与本地气候有关。种子被放置于一个较宽的温度范围(11-48℃)以及两个水分梯度处理中。我们发现,石茅的种子可以在很宽的温度范围下萌发,但在不同的种群中,种子萌发的比例随温度和水分的不同而有较大的变化。有证据表明,当石茅的生长范围从温暖的气候扩展到寒冷的气候时,种子萌发温度的生态位也同时发生了向低温的转变。我们的研究结果表明,石茅种子的萌发已经适应了当地的气候,使其在整个生长范围内的萌发最大化,这可能是其入侵新环境的一个重要贡献因素。

入侵植物根茎的生长和竞争力因相邻植物的不同而不同

物种内的遗传和表型变异对进化过程的影响已众所周知,但人们对种内变异如何影响群落水平过程还知之甚少。在人类对自然系统造成影响的大背景下,由于人类活动可能会产生巨大的选择压力,因此具有生态意义的种内变异可能会特别重要。在一项温室实验中,我们研究了一种分布广泛的入侵物种和农业杂草石茅(Sorghum halepense)在受到种间竞争、种内竞争和土壤肥力的影响时,其在生物量和根茎方面发生的种内变异和生态型变异。与我们的预期和此前的研究结果不同的是,我们并没有在这一早期生命阶段中发现石茅各生态型生物量的改变。然而,我们确实发现石茅的生物量会随着竞争植株种类和土壤施肥方式的不同而发生很显著的变化,同时不同株之间也存在很大差异。农业生态型的根茎较其它生态型大了11%,经施肥处理后的增大幅度更高至3倍;虽然施肥后的根茎生物量增加了~50%,但生态型之间却并无差异。有趣的是,当受到种内竞争时,与玉米(Zea mays)发生种间竞争时的情况相比,石茅的生物量和根茎生物量产出分别减少了32%和20%。我们的研究结果表明,针对相邻植株的种类而发生的物种特异性竞争响应以及根茎分配的改变,石茅在受竞争时可能会产生适应性响应,从而使分配情况发生改变。

Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice

Transposable elements(TEs)are a major force in the production of new alleles during domestication;nevertheless,their use in association studies has been limited because of their complexity.We have developed a TE genotyping pipeline(TEmarker)and applied it to whole-genome genome-wide association study(GWAS)data from 176 Oryza sativa subsp.japonica accessions to identify genetic elements associated with specific agronomic traits.TE markers recovered a large proportion(69%)of single-nucleotide polymorphism(SNP)-based GWAS peaks,and these TE peaks retained ca.25%of the SNPs.The use of TEs in GWASs may reduce false positives associated with linkage disequilibrium(LD)among SNP markers.A genome scan revealed positive selection on TEs associated with agronomic traits.We found several cases of insertion and deletion variants that potentially resulted from the direct action of TEs,including an allele of LOC_Os11g08410 associated with plant height and panicle length traits.Together,these findings reveal the utility of TE markers for connecting genotype to phenotype and suggest a potential role for TEs in influencing phenotypic variations in rice that impact agronomic traits.