An allelic variation in the promoter of the LRR-RLK gene,qSS6.1,is associated with melon seed size

Seed size is an important agronomic trait in melons that directly affects seed germination and subsequent seedling growth.However,the genetic mechanism underlying seed size in melon remains unclear.In the present study,we employed Bulked-Segregant Analysis sequencing(BSA-seq)to identify a candidate region(~1.35 Mb)on chromosome 6 that corresponds to seed size.This interval was confirmed by QTL mapping of three seed size-related traits from an F2 population across three environments.This mapping region represented nine QTLs that shared an overlapping region on chromosome 6,collectively referred to as qSS6.1.New InDel markers were developed in the qSS6.1 region,narrowing it down to a 68.35 kb interval that contains eight annotated genes.Sequence variation analysis of the eight genes identified a SNP with a C to T transition mutation in the promoter region of MELO3C014002,a leucine-rich repeat receptor-like kinase(LRR-RLK)gene.This mutation affected the promoter activity of the MELO3C014002 gene and was successfully used to differentiate the large-seeded accessions(C-allele)from the small-seeded accessions(T-allele).qRT-PCR revealed differential expression of MELO3C014002 between the two parental lines.Its predicted protein has typical LRR-RLK family domains,and phylogenetic analyses reveled its similarity with the homologs in several plant species.Altogether,these findings suggest MELO3C014002 as the most likely candidate gene involved in melon seed size regulation.Our results will be helpful for better understanding the genetic mechanism regulating seed size in melons and for genetically improving this important trait through molecular breeding pathways.

Allelic functional variation of FimH among Salmonella enterica subspecies

Salmonella enterica has a wide diversity,with numerous serovars belonging to six different subspecies with dynamic animal-host tropism.The FimH protein is the adhesin mediating binding to various cells,and slight amino acid discrepancy significantly affects the adherence capacities.To date,the general function of FimH variability across dif-ferent subspecies of Salmonella enterica has not been addressed.To investigate the biological functions of FimH among the six Salmonella enterica subspecies,the present study performed several assays to determine biofilm for-mation,Caenorhabditis elegans killing,and intestinal porcine enterocyte cell IPEC-J2 adhesion by using various FimH allele mutants.In general,allelic mutations in both the lectin and pilin domains of FimH could cause changes in bind-ing affnity,such as the N79S mutation.We also observed that the N79S variation in Salmonella Dublin increased the adhesive ability of IPEC-J2 cells.Moreover,a new amino acid substitution,T260M,within the pilin domain in one subspecies llb strain beneficial to binding to cells was highlighted in this study,even though the biofilm-forming and Caenorhabditis elegans-killing abilities exhibited no significant differences in variants.Combined with point muta-tions being a natural tendency due to positive selection in harsh environments,we speculate that allelic variation T26oM probably contributes to pathoadaptive evolution in Salmonella enterica subspecies llb.

Allelic Variation in Loci for Adaptive Response and Its Effect on Agronomical Traits in Chinese Wheat(Triticum aestivum L.)

Heading date was an important trait that decided the adaptation of wheat to environments. It was modiifed by genes involved in vernalization response, photoperiod response and development rate. In this study, four loci Xgwm261, Xgwm219, Xbarc23 and Ppd-D1 which were previously reported related to heading time were analyzed based on three groups of wheat including landraces （L）, varieties bred before 1983 （B82） and after 1983 （A83） collected from Chinese wheat growing areas. Generally, heading date of landrace was longer than that of varieties. Signiifcant differences in the heading time existed within the groups, which implied that diversiifcation selection was much helpful for adaptation in each wheat zone. Photoperiod insensitive allele Ppd-D1a was the ifrst choice for both landrace and modern varieties, which promoted the heading date about four days earlier than that of sensitive allele Ppd-D1b. The three SSR loci had different characters in the three groups. Predominant allele combination for each zone was predicted for wheat group L and A83, which made great contribution to advantageous traits. Xgwm219 was found to be signiifcantly associated with heading date in Yellow and Huai River Winter Wheat Zone （Zone II） and spike length in Middle and lower Yangtze Valley Winter Wheat Zone （Zone III）, which implied functional diversiifcation for adaption. Variation for earliness genes provided here will be helpful for whet breeding in future climatic change.

Detection of Allelic Variation in Chinese Wheat (Triticum aestivum L.) Germplasm with Drought ToleranceUsing SSR Markers

Allelic variation in two domestic wheat landraces, Pingyaobaimai and Mazhamai, two cornerstone breeding materials and their derived cultivars with drought tolerance was detected by SSR (simple sequence repeat) markers. The clustering of 25 accessions showed that the similarity between Pingyaobaimai and Yandal817, the latter was developed from the former, was 0.71, the highest one of all accessions, but the similarities were very low between these two accessions and other accessions including their derived cultivars. A similar situation was revealed between Mazhamai and its derived cultivars. Pingyaobaimai and its three derived cultivars shared three alleles at loci Xgwm526, Xgwm538 and Xgwm126 on chromosome arms 2BL, 4BL and 5AL, respectively. There were six shared alleles in Mazhamai and its derived cultivars, in order of Xgwm157, Xgwm126, Xgwm212, Xgwm626, Xgwm471 and Xgwm44 on chromosome arms 2DL, 5AL, 5DL, 6BL, 7AS and 7DC, respectively. Only one shared allele was detected between the pedigrees of Pingyaobaimai and Mazhamai. The difference of shared alleles in two cornerstone breeding materials and their derived cultivars revealed the diversity in Chinese wheat germplasm with drought tolerance and the complication in genetic basis of drought tolerance in wheat.

Identification of Multiple Alleles at the Wx Locus and Development of Single Segment Substitution Lines for the Alleles in Rice

The microsatellite markers 484/485 and 484/W2R were used to identify the multiple alleles at the Wx locus in rice germplasm. Fifteen alleles were identified in 278 accessions by using microsatellite class and G-T polymorphism. Among these alleles, （CT）12-G, （CT）15-G, （CT）16-G, （CT）17-G, （CT）18-G and （CT）21-G have not been reported. Seventy-two single-segment substitution lines （SSSLs） carrying different alleles at the Wx locus were developed by using Huajingxian 74 with the （CT）11-G allele as a recipient and 20 accessions containing 12 different alleles at the Wx locus as donors. The estimated length of the substituted segments ranged from 2.2 to 77.3 cM with an average of 17.4 cM.

Identification and Genetic Analysis of a Novel Allelic Variation of Brittle-1 with Endosperm Mutant in Maize

Endosperm mutants are critical to the studies on both starch synthesis and metabolism and genetic improvement of starch quality in maize.In the present study,a novel maize endosperm mutant A0178 of natural variation was used as the experimental material and identified and then characterized.Through phenotypic identification,genetic analysis,main ingredients measurement and embryo rescue,development of genetic mapping population from A0178,the endosperm mutant gene was located.The results showed that the mutant exhibited extremely low germination ability as attributed to the inhibited embryo development,and amounts of sugars were accumulated in the mutant seeds and more sugars content was detected at 23 days after pollination(DAP)in A0178 than B73.Employing genetic linkage analysis,the mutant trait was mapped in the bin 5.04 on chromosome 5.Sequence analysis showed that two sites of base transversion and insertion presented in the protein coding region and non-coding region of the mutant brittle-1(bt1),the adenylate translocator encoding gene involved in the starch synthesis.The single base insertion in the coding region cause frameshift mutation,early termination and lose of function of Brittle-1(BT1).All results suggested that bt1 is a novel allelic gene and the causal gene of this endosperm mutant,providing insights on the mechanism of endosperm formation in maize.

Haplotypic Structure and Allelic Variation of rab17,an ABA-Responsive Gene,in a Mini Core Set of Chinese Diversified Maize Inbred Lines

Drought stress is one of the most important factors limiting maize production. Rab17 is an ABA-responsive gene and associated with drought tolerance. In order to identify haplotypic structure and mine allelic variants at tab17 locus, nucleotide diversity and linkage disequilibrium （LD） structure of rab17 were evaluated among a mini core set of Chinese diversified maize inbred lines. Totally, 19 SNP and 18 insertion/deletions （InDels） were identified, among which 81% were in non-coding regions and 19% in coding regions. The results showed that a high level of diversity appeared within 1 kb upstream of the rabl 7 locus, and declined quickly downstream of the gene region. Rapid decay of linkage disequilibrium of rabl 7 region with distance within 1 kb was detected. Functional markers which can be developed based on haplotype 14 are expected to have contribution to molecular breeding for drought tolerance.

Functional divergences of natural variations of TaNAM-A1 in controlling leaf senescence during wheat grain filling

Leaf senescence is an essential physiological process related to grain yield potential and nutritional quality.Green leaf duration(GLD)after anthesis directly reflects the leaf senescence process and exhibits large genotypic differences in common wheat;however,the underlying gene regulatory mechanism is still lacking.Here,we identified TaNAM-A1 as the causal gene of the major loci q GLD-6A for GLD during grain filling by map-based cloning.Transgenic assays and TILLING mutant analyses demonstrated that TaNAM-A1 played a critical role in regulating leaf senescence,and also affected spike length and grain size.Furthermore,the functional divergences among the three haplotypes of TaNAM-A1 were systematically evaluated.Wheat varieties with TaNAM-A1d(containing two mutations in the coding DNA sequence of TaNAM-A1)exhibited a longer GLD and superior yield-related traits compared to those with the wild type TaNAM-A1a.All three haplotypes were functional in activating the expression of genes involved in macromolecule degradation and mineral nutrient remobilization,with TaNAM-A1a showing the strongest activity and TaNAM-A1d the weakest.TaNAM-A1 also modulated the expression of the senescencerelated transcription factors TaNAC-S-7A and TaNAC016-3A.TaNAC016-3A enhanced the transcriptional activation ability of TaNAM-A1a by protein–protein interaction,thereby promoting the senescence process.Our study offers new insights into the fine-tuning of the leaf functional period and grain yield formation for wheat breeding under various geographical climatic conditions.

Functional characterization of powdery mildew resistance gene MIIW172,a new Pm60 allele and its allelic variation in wild emmer wheat

Wild emmer wheat(Triticum dicoccoides,WEW)is an immediate progenitor of both the cultivated tetraploid and hexaploid wheats and it harbors rich genetic diversity against powdery mildew caused by Blumeria graminis f.sp.tritici(Bgt).A powdery mildew resistance gene Ml I^(W172)originated from WEW accession I^(W172)(G-797-M)is fine mapped in a 0.048 centimorgan(c M)genetic interval on 7 AL,corresponding to a genomic region spanning 233 kb,1 Mb and 800 kb in Chinese Spring,WEW Zavitan,and T.urartu G1812,respectively.Ml I^(W172)encodes a typical NLR protein NLRI^(W172)and physically locates in an NBS-LRR gene cluster.NLRI^(W172)is subsequently identified as a new allele of Pm60,and its function is validated by EMS mutagenesis and transgenic complementation.Haplotype analysis of the Pm60 alleles reveals diversifications in sequence variation in the locus and presence and absence variations(PAV)in WEW populations.Four common single nucleotide variations(SNV)are detected between the Pm60 alleles from WEW and T.urartu,indicative of speciation divergence between the two different wheat progenitors.The newly identified Pm60 alleles and haplotypes in WEW are anticipated to be valuable for breeding powdery mildew resistance wheat cultivars via marker-assisted selection.

Exome-wide variation in a diverse barley panel reveals genetic associations with ten agronomic traits in Eastern landraces

Barley(Hordeum vulgare ssp.vulgare)is one of the first crops to be domesticated and is adapted to a wide range of environments.Worldwide barley germplasm collections possess valuable allelic variations that could further improve barley productivity.Although barley genomics has offered a global picture of allelic variation among varieties and its association with various agronomic traits,polymorphisms from East Asian varieties remain scarce.In this study,we analyze exome polymorphisms in a panel of 274 barley varieties collected worldwide,including 137 varieties from East Asian countries and Ethiopia.We reveal the underlying population structure and conduct genome-wide association studies for 10 agronomic traits.Moreover,we examin genome-wide associations for traits related to grain size such as awn length and glume length.Our results demonstrate the value of diverse barley germplasm panels containing Eastern varieties,highlighting their distinct genomic signatures relative to Western subpopulations.

Reviewing Self-Injuries Behavior in Macaques: The Role of Early Experience and Genetics in an Integrated Non-Human Model

Genetic differences in non-human primates and the context where they were reared are important in the determination of their behaviors. Some studies suggest that Self-Injurious Behavior results from stress or anxiety, but some macaques appear to be more vulnerable to acquiring Self-Injurious Behavior. Vulnerability and risk for socially reared macaques of developing Self-Injurious Behavior increased when they experienced early adverse events and suffered from consequent stress. Stressful events can cause alterations in the neuroendocrine and neuropeptide systems associated with the regulation of stress and anxiety. Dysregulation in these systems contributes to the occurrence of anxious episodes that lead to self-harm. This could be used by those animals to counteract the effects of anxiety, causing euphoria by releasing endogenous opioids. In developing an integrative approach of Self-Injurious Behavior, we propose the diathesis-stress model to illustrate how the environment and genetics are influenced as well, taking rhesus monkeys as an example. Rhesus macaques and humans have essentially the same gene 5-HTT as well as functional polymorphism. The allelic variation in the region promoting the serotonin transporter gene (5-HTT) was associated with significant differences in the number of depressive symptoms and contributions to social reward and punishment. Growing up without the mother and the rearing environment are important risk factors for developing abnormal behaviors. The main idea is that monkeys who carry short 5-HTT allele and are reared with their peers (without their mother) suffer from

A rare Waxy allele coordinately improves rice eating and cooking quality and grain transparency

In rice(Oryza sativa), amylose content(AC) is the major factor that determines eating and cooking quality(ECQ). The diversity in AC is largely attributed to natural allelic variation at the Waxy(Wx)locus. Here we identified a rare Wx allele, Wx^(mw) ,which combines a favorable AC, improved ECQ and grain transparency. Based on a phylogenetic analysis of Wx genomic sequences from 370 rice accessions, we speculated that Wx^(mw) may have derived from recombination between two important natural Wx alleles, Wx^(in) and Wx^(b). We validated the effects of Wx^(mw) on rice grain quality using both transgenic lines and near-isogenic lines(NILs). When introgressed into the japonica Nipponbare(NIP) background, Wx^(mw) resulted in a moderate AC that was intermediate between that of NILs carrying the Wx^(b)allele and NILs with the Wx^(mp) allele. Notably, mature grains of NILs fixed for Wx^(mw) had an improved transparent endosperm relative to soft rice. Further, we introduced Wx^(mw) into a high-yielding japonica cultivar via molecular marker-assisted selection: the introgressed lines exhibited clear improvements in ECQ and endosperm transparency. Our results suggest that Wx^(mw) is a promising allele to improve grain quality, especially ECQ and grain transparency of high-yielding japonica cultivars, in rice breeding programs.

Novel Natural Allelic Variations at the Rht-1 Loci in Wheat

Plant height is an important agronomic trait. Dramatic increase in wheat yield during the ＂green revolution＂ is mainly due to the widespread utilization of the Reduced height （Rht）-1gene. We analyzed the natural allelic variations of three homoeologous loci Rht-A1, Rht-B1, and Rht-D1 in Chinese wheat （Triticum aestivum L.） micro-core collections and the Rht-B1/D1 genotypes in over 1,500 bred cultivars and germplasms using a modified EcoTILLING. We identified six new Rht-A1 allelic variations （Rht-Alb-g）, eight new Rht-B1 allelic variations （Rht-Blh-o）, and six new Rht-D1 allelic variations （Rht-Dle-j）. These allelic variations contain single nucleotide polymorphisms （SNPs） or small insertions and deletions in the coding or uncoding regions, involving two frame-shift mutations and 15 missenses. Of which, Rht-Dle and Rht-Dlh resulted in the loss of interactions of GID1-DELLA-GID2, Rht-Blicould increase plant height. We found that the Rht-Blh contains the same SNPs and 197 bp fragment insertion as reported in Rht-Blc. Further detection of Rht-Blh in Tibet wheat germplasms and wheat relatives indicated that Rht-Blc may originate from Rht-Blh. These results suggest rich genetic diversity at the Rht-1 loci and provide new resources for wheat breeding.

The metal tolerance protein OsMTP11 facilitates cadmium sequestration in the vacuoles of leaf vascular cells for restricting its translocation into rice grains

Rice(Oryza sativa)provides>20%of the consumed calories in the human diet.However,rice is also a leading source of dietary cadmium(Cd)that seriously threatens human health.Deciphering the genetic network that underlies the grain-Cd accumulation will benefit the development of low-Cd rice and mitigate the effects of Cd accumulation in the rice grain.In this study,we identified a QTL gene,OsCS1,which is allelic to OsMTP11 and encodes a protein sequestering Cd in the leaf during vegetative growth and preventing Cd from being translocated to the grain after heading in rice.OsCS1 is predominantly expressed in leaf vascular parenchyma cells,where it binds to a vacuole-sorting receptor protein OsVSR2 and is translocated intracellularly from the trans-Golgi network to pre-vacuolar compartments and then to the vacuole.In this trafficking process,OsCS1 actively transports Cd into the endomembrane system and sequesters it in the vacuoles.There are natural variations in the promoter of OsCS1 between the indica and japonica rice subspecies.Duplication of a G-box-like motif in the promoter region of the superior allele of OsCS1 from indica rice enhances the binding of the transcription factor OsIRO2 to the OsCS1 promoter,thereby promoting OsCS1 expression.Introgression of this allele into commercial rice varieties could significantly lower grain-Cd levels compared to the inferior allele present in japonica rice.Collectively,our findings offer new insights into the genetic control of leaf-to-grain Cd translocation and provide a novel gene and its superior allele for the genetic improvement of low-Cd variety in rice.

The origin of Wx^(la) provides new insights into the improvement of grain quality in rice

Appearance and taste are important factors in rice(Oryza sativa) grain quality. Here, we investigated the taste scores and related eating-quality traits of533 diverse cultivars to assess the relationships between—and genetic basis of—rice taste and eating-quality. A genome-wide association study highlighted the Wx gene as the major factor underlying variation in taste and eating quality. Notably, a novel waxy(Wx) allele, Wx^(la), which combined two mutations from Wx^(b) and Wx^(in), exhibited a unique phenotype. Reduced GBSSI activity conferred Wx^(la) rice with both a transparent appearance and good eating quality. Haplotype analysis revealed that Wx^(la) was derived from intragenic recombination. In fact,the recombination rate at the Wx locus was estimated to be 3.34 kb/c M, which was about 75-fold higher than the genome-wide mean, indicating that intragenic recombination is a major force driving diversity at the Wx locus. Based on our results, we propose a new network for Wx evolution, noting that new Wx alleles could easily be generated by crossing genotypes with different Wx alleles. This study thus provides insights into the evolution of the Wx locus and facilitates molecular breeding for quality in rice.