Updating the elite rice variety Kongyu 131 by improving the <Emphasis Type="Italic">Gn1a</Emphasis> locus

Background

Kongyu 131 is an elite japonica rice variety of Heilongjiang Province, China. It has the characteristics of early maturity, superior quality, high yield, cold tolerance and wide adaptability. However, there is potential to improve the yield of Kongyu 131 because of the relatively few grains per panicle compared with other varieties. Hence, we rebuilt the genome of Kongyu 131 by replacing the GRAIN NUMBER1a (Gn1a) locus with a high-yielding allele from a big panicle indica rice variety, GKBR. High-resolution melting (HRM) analysis was used for single nucleotide polymorphism (SNP) genotyping.

Results

Quantitative trait locus (QTL) analysis of the BC₃F₂ population showed that the introgressed segment carrying the Gn1a allele of GKBR significantly increased the branch number and grain number per panicle. Using 5 SNP markers designed against the sequence within and around Gn1a, the introgressed chromosome segment was shortened to approximately 430 Kb to minimize the linkage drag by screening recombinants in the target region. Genomic components of the new Kongyu 131 were detected using 220 SNP markers evenly distributed across 12 chromosomes, suggesting that the recovery ratio of the recurrent parent genome (RRPG) was 99.89%. Compared with Kongyu 131, the yield per plant of the new Kongyu 131 increased by 8.3% and 11.9% at Changchun and Jiamusi, respectively.

Conclusions

To achieve the high yield potential of Kongyu 131, a minute chromosome fragment carrying the favorable Gn1a allele from the donor parent was introgressed into the genome of Kongyu 131, which resulted in a larger panicle and subsequent yield increase in the new Kongyu 131. These results indicate the feasibility of improving an undesirable trait of an elite variety by replacing only a small chromosome segment carrying a favorable allele.

     

An Evaluation of two <Emphasis Type="Italic">H1</Emphasis>-Linked Markers and their Suitability for Selecting <Emphasis Type="Italic">Globodera rostochiensis</Emphasis> Resistant Potatoes in the New York Breeding Program

The golden cyst nematode (Globodera rostochiensis) is a serious pest that can dramatically reduce potato crop yield. Pathotype Ro1 of G. rostochiensis was first detected in the United States in 1941 and is still present on several farms in New York State. The H1 gene confers high levels of resistance to pathotype Ro1 but screening for it with a bioassay is time consuming and expensive. In this study two known molecular markers, 57R and TG689, were evaluated for their ability to identify resistant clones among 38 global cultivars and 350 New York breeding clones. The ability of either marker to predict resistance was high – 99.7% and 98.3% for 57R and TG689, respectively – but the ability to predict susceptibility was much lower, 47% and 41%, respectively. As resistance is the trait of interest, either of these markers is sufficient to make selection decisions in a practical breeding program. Cases exhibiting discordance between presence/absence of diagnostic markers and bioassay results were investigated further. Recombination, inflow of other resistance genes, and occasional failure of marker- and/or bio-assays are discussed as potential causes.     

A novel Rice QTL <Emphasis Type="Italic">qOPW11</Emphasis> Associated with Panicle Weight Affects Panicle and Plant Architecture

Background

The improvement of rice yield is a crucial global issue, but evaluating yield requires substantial efforts. Rice yield comprises the following indices: panicle number (PN), grain number per panicle (GN), 1000-grain weight, and percentage of ripened grain. To simplify measurements, we analyzed one panicle weight (OPW) as a simplified yield index that integrates GN, grain weight, and percentage of ripened grain, and verified its suitability as a proxy for GN and grain weight in particular.

Results

Quantitative trait locus (QTL) analysis using 190 recombinant inbred lines derived from Koshihikari (large panicle and small grain) and Yamadanishiki (small panicle and large grain), japonica cultivars detected three QTLs on chromosomes 5 (qOPW5), 7 (qOPW7) and 11 (qOPW11). Of these, qOPW5 and qOPW11 were detected over two years. qOPW5 and qOPW7 increased OPW, and qOPW11 decreased it at Yamadanishiki alleles. A chromosome segment substitution line (CSSL) with a genomic segment from Yamadanishiki substituted in the Koshihikari genetic background harboring qOPW5 increased grain weight. qOPW11 had the largest genetic effect of QTLs, which was validated using a CSSL. Substitution mapping using four CSSLs revealed that qOPW11 was located in the range of 1.46 Mb on chromosome 11. The CSSL harboring qOPW11 decreased primary and secondary branch numbers, culm length, and panicle length, and increased PN.

Conclusions

In this study, three QTLs associated with OPW were detected. The CSSL with the novel and largest QTL, qOPW11, differed in some traits associated with both panicle and plant architecture, indicating different functions for the meristem in the vegetative versus the reproductive stages. qOPW5 coincided with an identified QTL for grain width and grain weight, suggesting that qOPW5 was affected by rice grain size. OPW can be considered a useful trait for efficient detection of QTLs associated with rice yield.

     

Development of a Potato Cultivar (<Emphasis Type="Italic">Solanum tuberosum</Emphasis> L.) Core Collection,a Valuable Tool to Prospect Genetic Variation for Novel Traits

This study presents the development of a core collection capturing the genetic diversity of a collection of 350 tetraploid cultivated potato varieties (Solanum tuberosum L.). The core collection was established by using simple sequence repeats (SSR) data and the M strategy, which aims at maximizing the allelic diversity. A 48-core collection was defined which captured 99.5% of the SSR alleles used to establish it, and 96.9% of the SSR alleles which belonged to an independent set of markers. The defined core collection was further validated by analysing 35 agro-morphological traits. The class coverage value and the estimates of the Shannon-Weaver diversity index indicated a good representation of the phenotypic diversity in the core collection. Furthermore, the core set included accessions having the most desirable status for several agronomic traits. A linkage disequilibrium (LD) analysis, using data obtained with the SolCAP SNP array on the defined core collection, was performed. The population structure analysis showed that the core collection did not present a clear genetic structure. The linkage disequilibrium analysis carried out between markers located on the same pseudomolecule within 10,000 bp concluded that 41.3% of these pairs of SNP markers have a significant LD. We conclude that this core collection, representative of the genetic diversity of cultivated potato varieties, is a relevant tool for a first screening for genetic variation regarding novel traits of interest.     

Rooting Characteristics of <Emphasis Type="Italic">Solanum chacoense</Emphasis> and <Emphasis Type="Italic">Solanum tuberosum in Vitro</Emphasis>

The precise level of environmental control in vitro may aid in identifying genetically superior plant germplasm for rooting characteristics (RC) linked to increased foraging for plant nitrogen (N). The objectives of this research were to determine the phenotypic variation in root morphological responses of 49 Solanum chacoense (chc), 30 Solanum tuberosum Group Phureja – Solanum tuberosum Group Stenotomum (phu-stn), and three Solanum tuberosum (tbr) genotypes to 1.0 and 0.5 N rate in vitro for 28 d, and identify genotypes with superior RC. The 0.5 N significantly increased density of root length, surface area, and tips. All RC were significantly greater in chc than in either phu-stn or tbr. Based upon clustering on root length, surface area, and volume, the cluster with the greatest rooting values consisted of eight chc genotypes that may be utilized to initiate a breeding program to improve RC in potato.     

Genome-wide association mapping for root cone angle in rice

Background

Plant root systems play a major role in anchoring and in water and nutrient uptake from the soil. The root cone angle is an important parameter of the root system architecture because, combined with root depth, it helps to determine the volume of soil explored by the plant. Two genes, DRO1 and SOR1, and several QTLs for root cone angle have been discovered in the last 5 years.

Results

To find other QTLs linked to root cone angle, a genome-wide association mapping study was conducted on two panels of 162 indica and 169 japonica rice accessions genotyped with two sets of SNP markers (genotyping-by-sequencing set with approximately 16,000 markers and high-density-rice-array set with approximately 300,000 markers). The root cone angle of all accessions was measured using a screen protractor on images taken after 1 month of plant growth in the Rhizoscope phenotyping system. The distribution of the root cone angle in the indica panel was Gaussian, but several accessions of the japonica panel (all the bulus from Indonesia and three temperate japonicas from Nepal or India) appeared as outliers with a very wide root cone angle. The data were submitted to association mapping using a mixed model with control of structure and kinship. A total of 15 QTLs for the indica panel and 40 QTLs for the japonica panel were detected. Genes underlying these QTLs (+/?50 kb from the significant markers) were analyzed. We focused our analysis on auxin-related genes, kinases, and genes involved in root developmental processes and identified 8 particularly interesting genes.

Conclusions

The present study identifies new sources of wide root cone angle in rice, proposes ways to bypass some drawbacks of association mapping to further understand the genetics of the trait and identifies candidate genes deserving further investigation.

     

Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications

Background

Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit “sweet spot” for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups. This paper summarizes results from large-scale deployment of an Illumina 6 K SNP array for rice.

Results

Design of the Illumina Infinium 6 K SNP chip for rice, referred to as the Cornell_6K_Array_Infinium_Rice (C6AIR), includes 4429 SNPs from re-sequencing data and 1571 SNP markers from previous BeadXpress 384-SNP sets, selected based on polymorphism rate and allele frequency within and between target germplasm groups. Of the 6000 attempted bead types, 5274 passed Illumina’s production quality control. The C6AIR was widely deployed at the International Rice Research Institute (IRRI) for genetic diversity analysis, QTL mapping, and tracking introgressions and was intensively used at Cornell University for QTL analysis and developing libraries of interspecific chromosome segment substitution lines (CSSLs) between O. sativa and diverse accessions of O. rufipogon or O. meridionalis. Collectively, the array was used to genotype over 40,000 rice samples. A set of 4606 SNP markers was used to provide high quality data for O. sativa germplasm, while a slightly expanded set of 4940 SNPs was used for O. sativa X O. rufipogon populations. Biparental polymorphism rates were generally between 1900 and 2500 well-distributed SNP markers for indica x japonica or interspecific populations and between 1300 and 1500 markers for crosses within indica, while polymorphism rates were lower for pairwise crosses within U.S. tropical japonica germplasm. Recently, a second-generation array containing ~7000 SNP markers, referred to as the C7AIR, was designed by removing poor-performing SNPs from the C6AIR and adding markers selected to increase the utility of the array for elite tropical japonica material.

Conclusions

The C6AIR has been successfully used to generate rapid and high-quality genotype data for diverse genetics and breeding applications in rice, and provides the basis for an optimized design in the C7AIR.

     

Phenotypic and Genomic Modifications Associated with <Emphasis Type="Italic">Globodera pallida</Emphasis> Adaptation to Potato Resistances

Studying phenotypic and genomic modifications associated with pathogen adaptation to resistance is a crucial step to better understand and anticipate resistance breakdown. This short review summarizes recent results obtained using experimentally evolved populations of the potato cyst nematode Globodera pallida. In a first step, the variability of resistance durability was explored in four different potato genotypes carrying the resistance quantitative trait loci (QTL) GpaV_vrn originating from Solanum vernei but differing by their genetic background. The consequences of the adaptation to resistance in terms of local adaptation, cross-virulence and virulence cost were then investigated. Finally, a genome scan approach was performed in order to identify the genomic regions involved in this adaptation. Results showed that nematode populations were able to adapt to the QTL GpaV_vrn, and that the plant genetic background has a strong impact on resistance durability. A trade-off between the adaptations to different resistant potato genotypes was detected, and we also showed that adaptation to the resistance QTL GpaV_vrn from S. vernei did not allow adaptation to the colinear locus from S. sparsipilum (GpaV_spl). Unexpectedly, the adaptation to resistance led to an increase of virulent individual’s fitness on a susceptible host. Moreover, the genome scan approach allowed the highlighting of candidate genomic regions involved in adaptation to host plant resistance. This review shows that experimental evolution is an interesting tool to anticipate the adaptation of pathogen populations and could be very useful for identifying durable strategies for resistance deployment.     

QTL Analysis of Tuber Dormancy and Sprouting in Potato

Tuber dormancy and sprouting are important traits in commercial potato varieties. Since wild Solanum species can contribute new alleles in breeding, we combined Solanum chacoense and S. berthaultii species in a mapping population to develop a linkage map with genome wide markers and identify quantitative trait loci (QTL) for tuber dormancy and sprouting. There was genetic variation for the evaluated traits and high correlation (0.80) between dormancy and apical dominance release. QTL for tuber dormancy and sprouting traits were mapped to the same or similar positions on chromosomes 2, 3, 5, and 7, explaining from 9.5% to 16.3% of the phenotypic variance. We identified candidate genes associated with all major phytohormone regulation in close linkage with the QTL. The QTL on chromosomes 2, 3 and 7 are good candidates for marker assisted breeding, since they were associated with dormancy and apical dominance release and should be useful to delay or accelerate tuber sprouting.     

Genome-wide association study and candidate gene analysis of rice cadmium accumulation in grain in a diverse rice collection

Background

Cadmium (Cd) accumulation in rice followed by transfer to the food chain causes severe health problems in humans. Breeding of low Cd accumulation varieties is one of the most economical ways to solve the problem. However, information on the identity of rice germplasm with low Cd accumulation is limited, particularly in indica, and the genetic basis of Cd accumulation in rice is not well understood.

Results

Screening of 312 diverse rice accessions revealed that the grain Cd concentrations of these rice accessions ranged from 0.12 to 1.23?mg/kg, with 24 accessions less than 0.20?mg/kg. Three of the 24 accessions belong to indica. Japonica accumulated significantly less Cd than indica (p < 0.001), while tropical japonica accumulated significantly less Cd than temperate japonica (p < 0.01). GWAS in all accessions identified 14 QTLs for Cd accumulation, with 7 identified in indica and 7 identified in japonica subpopulations. No common QTL was identified between indica and japonica. The previously identified genes (OsHMA3, OsNRAMP1, and OsNRAMP5) from japonica were colocalized with QTLs identified in japonica instead of indica. Expression analysis of OsNRAMP2, the candidate gene of the novel QTL (qCd3–2) identified in the present study, demonstrated that OsNRAMP2 was mainly induced in the shoots of high Cd accumulation accessions after Cd treatment. Four amino acid differences were found in the open reading frame of OsNRAMP2 between high and low Cd accumulation accessions. The allele from low Cd accumulation accessions significantly increased the Cd sensitivity and accumulation in yeast. Subcellular localization analysis demonstrated OsNRAMP2 expressed in the tonoplast of rice protoplast.

Conclusion

The results suggest that grain Cd concentrations are significantly different among subgroups, with Cd concentrations decreasing from indica to temperate japonica to tropical japonica. However, considerable variations exist within subgroups. The fact that no common QTL was identified between indica and japonica implies that there is a different genetic basis for determining Cd accumulation between indica and japonica, or that some QTLs for Cd accumulation in rice are subspecies-specific. Through further integrated analysis, it is speculated that OsNRAMP2 could be a novel functional gene associated with Cd accumulation in rice.

     

Identification and fine mapping of a new gene, <Emphasis Type="Italic">BPH31</Emphasis> conferring resistance to brown planthopper biotype 4 of India to improve rice, <Emphasis Type="Italic">Oryza sativa</Emphasis> L

Background

Rice (Oryza sativa L.) is the staple food for more than 3.5 billion people, mainly in Asia. Brown planthopper (BPH) is one of the most destructive insect pests of rice that limits rice production. Host-plant resistance is one of the most efficient ways to overcome BPH damage to the rice crop.

Results

BPH bioassay studies from 2009 to 2015 conducted in India and at the International Rice Research Institute (IRRI), Philippines, revealed that the cultivar CR2711–76 developed at the National Rice Research Institute (NRRI), Cuttack, India, showed stable and broad-spectrum resistance to several BPH populations of the Philippines and BPH biotype 4 of India. Genetic analysis and fine mapping confirmed the presence of a single dominant gene, BPH31, in CR2711–76 conferring BPH resistance. The BPH31 gene was located on the long arm of chromosome 3 within an interval of 475 kb between the markers PA26 and RM2334. Bioassay analysis of the BPH31 gene in CR2711–76 was carried out against BPH populations of the Philippines. The results from bioassay revealed that CR2711–76 possesses three different mechanisms of resistance: antibiosis, antixenosis, and tolerance. The effectiveness of flanking markers was tested in a segregating population and the InDel type markers PA26 and RM2334 showed high co-segregation with the resistance phenotype. Foreground and background analysis by tightly linked markers as well as using the Infinium 6 K SNP chip respectively were applied for transferring the BPH31 gene into an indica variety, Jaya. The improved BPH31-derived Jaya lines showed strong resistance to BPH biotypes of India and the Philippines.

Conclusion

The new BPH31 gene can be used in BPH resistance breeding programs on the Indian subcontinent. The tightly linked DNA markers identified in the study have proved their effectiveness and can be utilized in BPH resistance breeding in rice.

     

Effective Management of the <Emphasis Type="Italic">Phthorimaea operculella</Emphasis> (Zeller) Using PVA Nanofibers Loaded with <Emphasis Type="Italic">Cinnamomum zeylanicum</Emphasis> Essential Oil

Phthorimaea operculella (Zeller) is one of the most common insect pests of cultivated potato in tropical and subtropical regions. In this research, a potential strategy to improve the insecticidal activity of plant essential oils for the effective management of P. operculella was studied. The insecticidal and residual effects of nanofiber oil (NFO) and pure essential oil (PEO) of Cinnamomum zeylanicum were assessed on PTM under laboratory conditions. The nanofibers were made by the electrospinning method using polyvinyl alcohol (PVA) polymer. The morphological characteristics of the nanofibers were evaluated by scanning electron microscopy and Fourier transform infrared spectroscopy. The chemical constituents of cinnamon essential oil (EO) were detected by GC/MS. Fumigant toxicity of NFO and PEO were evaluated on different growth stages (egg, male and female adults) of P. operculella. SEM and FTIR analyses confirmed the presence of EO on the nanofiber structure. The yield of the EO from C. zelanicum on the nanofibers was 1.86%. GC/MS analysis showed that cinnamaldehyde was the primary constituent (69.88%) of cinnamon EO. LC₅₀ values of C. zelanicum EO and NFO were 4.92 and 1.76 μl/l air for eggs, 0.444 and 0.212 μl/l air for female adults, and 0.424 and 0.192 μl/l air for male adults, respectively. Fumigant bioassays revealed that NFO was more toxic than C. zeylanicum oil against at all stages of P. operculella. The residual effect of PEO and NFO was evaluated against the egg stage of the P. operculella. NFO lost insecticidal effectiveness 47 days after application, while the efficacy of PEO decreased 15 days after application. Our results suggest that NFO of C. zeylanicum can be used as an effective new tool for the management of P. operculella.     

Transmission Efficiency of <Emphasis Type="Italic">Potato Leafroll Virus</Emphasis> by Four Potato Colonizing Aphid Species in Tunisian Potato Fields

This study investigated the transmission efficiency of Potato leafroll virus (PLRV) by four potato colonizing aphid species, Myzus persicae, Macrosiphum euphorbiae, Aphis gossypii and Aphis fabae, reported from leaves and yellow water trap. Physalis floridana was used as a test plant for virus transmission. DAS-ELISA was used for virus screening of samples as well as virus detection on the test plant after transmission experiment. A 2-h period was sufficient for the tested aphids to acquire PLRV virions. However, a difference in the transmission potential occurred according to the aphid species. The highest potential was recorded for M. persicae and M. euphorbiae, at 90 and 80%, respectively. For the first time, the study revealed the PLRV transmission efficiency of A. fabae, estimated at 50%. The lowest potential rate of 30% was recorded for A. gossypii. This study highlights the PLRV transmission capacities of four potato colonizing aphids suspected to play a key role in the spread of PLRV in potato seed production sites.     

Amplification of the <Emphasis Type="Italic">Phytophthora infestans</Emphasis> RG57 loci Facilitates <Emphasis Type="Italic">in planta</Emphasis> T-RFLP Identification of Late Blight Genotypes

Late blight, caused by the oomycete Phytophthora infestans (Mont.) de Bary, is a devastating disease in potato and tomato and causes yield and quality losses worldwide. The disease first emerged in central America and has since spread in North America including the United States and Canada. Several new genotypes of P. infestans have recently emerged, including US-22, US-23 and US-24. Due to significant economic and environmental impacts, there has been an increasing interest in the rapid identification of P. infestans genotypes. In addition to providing details regarding the various phenotypic characteristics such as fungicide resistance, host preference, and pathogenicity associated with various P. infestans genotypes, information related to pathogen movement and potential recombination may also be determined from the genetic analyses. Restriction fragment length polymorphism (RFLP) analysis with the RG57 loci is one of the most reliable procedures used to genotype P. infestans. However, the RFLP procedure requires propagation and isolation of the pathogen and relatively large amounts of DNA. Isolation of the late blight pathogen is sometimes impossible due to the poor condition of the infected tissues or the presence of fungicide residues. In this study, we describe a procedure to identify P. infestans at the molecular level in planta using terminal restriction fragment length polymorphism (T-RFLP) of the RG57 loci. This T-RFLP assay is sufficiently sensitive to detect and differentiate P. infestans genotypes directly in planta without propagation and isolation of the pathogen, to facilitate the timely implementation of best management practices.     

Genetic Diversity of Pathogenic <Emphasis Type="Italic">Fusarium semitectum</Emphasis> Isolates from Potato Tubers,Using PCR-IGS-RFLP Markers

Fusarium semitectum is one of the important causal agents of dry rot of potato tubers in the world. In order to determine genetic variability among 41 isolates of F. semitectum, morphological and molecular studies were carried out. All F. semitectum isolates were recovered from infected potato tubers with dry rot symptoms collected from four provinces in Iran. According to macroscopic and microscopic characteristics, 41 isolates of F. semitectum were classified in two morphotypes (morphotypes I and II). All 41 isolates were evaluated for their pathogenicity on healthy potato tubers. Tuber rot symptoms were observed on the 21st day after inoculation of Fusarium isolates on the tubers tested. The measurement was done by comparing the depth and width of lesion expansion among the isolates. Molecular characterization through PCR-IGS-RFLP analysis by six restriction enzymes (AluI, BsuRI, Eco88I, MspI, TaqI and PstI) divided the 41 isolates of F. semitectum into two separated clusters that were in accordance with the morphological characterization.     

Seasonal deviation effects foliar endophyte assemblage and diversity in <Emphasis Type="Italic">Asparagus racemosus</Emphasis> and <Emphasis Type="Italic">Hemidesmus indicus</Emphasis>

Background

Fungal endophytes are the living symbionts which cause no apparent damage to the host tissue. The distribution pattern of these endophytes within a host plant is mediated by environmental factors. This study was carried out to explore the fungal endophyte community and their distribution pattern in Asparagus racemosus and Hemidesmus indicus growing in the study area.

Results

Foliar endophytes were isolated for 2 years from A. racemosus and H. indicus at four different seasons (June–August, September–November, December–February, March–May). A total of 5400 (675/season/year) leaf segments harbored 38 fungal species belonging to 17 genera, 12 miscellaneous mycelia sterile from 968 isolates and 13 had yeast like growth. In A. racemosus, Acremonium strictum and Phomopsis sp.1, were dominant with overall relative colonization densities (RCD) of 7.11% and 5.44% respectively, followed by Colletotrichum sp.3 and Colletotrichum sp.1 of 4.89% and 4.83% respectively. In H. indicus the dominant species was A. strictum having higher overall RCD of 5.06%, followed by Fusarium moniliforme and Colletotrichum sp.2 with RCD of 3.83% and 3%, respectively. Further the overall colonization and isolation rates were higher during the wet periods (September–November) in both A. racemosus (92.22% and 95.11%) and H. indicus (82% and 77.11%).

Conclusion

Study samples treated with 0.2% HgCl₂ and 75% EtOH for 30 s and 1 min, respectively, confirmed most favorable method of isolation of the endophytes. Owing to high mean isolation and colonization rates, September–November season proved to be the optimal season for endophyte isolation in both the study plants. Assessing the bioactive potential of these endophytes, may lead to the isolation of novel natural products and metabolites.

     

Resistance to <Emphasis Type="Italic">Meloidogyne chitwoodi</Emphasis> Identified in Wild Potato Species

Meloidogyne chitwoodi (Columbia root-knot nematode, CRKN) can cause serious damage in potato production systems, decreasing tuber value in the fresh market and processing industries. Genetic resistance to CRKN was first identified from the wild diploid potato species Solanum bulbocastanum accession SB22 and was successfully introgressed into tetraploid potato breeding material. To expand the base of genetic resistance, 40 plant accessions representing nine wild potato species were screened for their resistance to M. chitwoodi. Greenhouse screening identified fifteen clones from S. hougasii, one clone from S. bulbocastanum, and one clone from S. stenophyllidium with moderate to high levels of resistance against three isolates of M. chitwoodi. Geographical mapping showed that the resistance sources identified in this and previous studies primarily originated in the states of Jalisco and Michoacán in west-central Mexico. These new sources of resistance will be introgressed into elite potato populations to facilitate the development of potato cultivars with durable resistance to M. chitwoodi.     

Dissection and fine-mapping of two QTL for grain size linked in a 460-kb region on chromosome 1 of rice

Background

Grain size is a key determinant of grain weight and a trait having critical influence on grain quality in rice. While increasing evidences are shown for the importance of minor-effect QTL in controlling complex traits, the attention has not been given to grain size until recently. In previous studies, five QTL having small effects for grain size were resolved on the long arm of chromosome 1 using populations derived from indica rice cross Zhenshan 97///Zhenshan 97//Zhenshan 97/Milyang 46. One of them, qTGW1.2c that was located in a 2.1-Mb region, was targeted for fine-mapping in the present study.

Results

Firstly, the qTGW1.2c region was narrowed down into 1.1 Mb by determining genotypes of the cross-over regions using polymorphic markers newly developed. Then, one BC₂F₉ plant that was only heterozygous in the updated QTL region was identified. A total of 12 populations in generations from BC₂F_11:12 to BC₂F_15:16 were derived and used for QTL mapping. Two QTL linked in a 460-kb region were separated. The qGS1-35.2 was delimited into a 57.7-kb region, containing six annotated genes of which five showed nucleotide polymorphisms between the two parental lines. Quantitative real-time PCR detected expression differences between near isogenic lines for qGS1-35.2 at three of the six annotated genes. This QTL affected grain length and width with opposite allelic directions, exhibiting significant effect on ratio of grain length to width but showing little influence on yield traits. The other QTL, qGW1-35.5, was located within a 125.5-kb region and found to primarily control grain width and consequently affect grain weight.

Conclusions

Our work lays a foundation for cloning of two minor QTL for grain size that have potential application in rice breeding. The qGS1-35.2 could be used to modify grain appearance quality without yield penalty because it affects grain shape but hardly influences grain yield, while qGW1-35.5 offers a new gene recourse for enhancing grain yield since it contributes to grain size and grain weight simultaneously.