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Persimmon is classified as either pollination-constant non-astringent (PCNA) or non-PCNA on the basis of the loss of astringency in fruit. PCNA trait of persimmon has attracted much research attention owing to its economical merit, as there is no cost in removing astringency. To efficiently develop new PCNA cultivars in crossbreeding, marker-assisted selection plays a crucial role. Here, we describe a cleaved amplified polymorphic sequence (CAPS) marker that can be used to select PCNA persimmon. A sequence-characterized amplified region (SCAR) marker used to screen for PCNA offspring is unsuitable for populations recently derived from two non-PCNA parents ('Yoshidagosho' and 'Toyoichi'), resulting in the selection of non-PCNA offspring as PCNA. To detect specific polymorphisms for these non-PCNA offspring, we analyzed fragment sizes of SCAR marker products by capillary DNA sequencing. A slightly lower-molecular-weight fragment at 353 bp was specifically detected in non-PCNA offspring but not in PCNA offspring. We treated the SCAR marker products with the StuI restriction enzyme and demonstrated that the smaller 353-bp fragment corresponded to allele a353-1, one of four previously identified sequence polymorphisms at the 353-bp peak, and a353-1 is linked to non-PCNA trait. Comprehensive analysis of 130 germplasms by the CAPS marker, detecting the truncated fragment after StuI treatment, indicated the presence of a353-1 in 38 non-PCNA cultivars. Our findings suggest the potential use of the CAPS marker for selecting PCNA offspring derived from these 38 non-PCNA cultivars. [ABSTRACT FROM AUTHOR]

Genotyping by sequencing (GBS) and single nucleotide polymorphism (SNP) chip technologies are the primary SNP genotyping technologies used today. However, these genotyping technologies have some drawbacks that limit their usefulness in analysis. We have developed a robust protocol called genotyping by multiplexed sequencing (GMS) using SNP markers, providing informative genotypic data with greater flexibility. The genotypes derived from direct sequence reads reduce ambiguity in genetic analysis. The advantages of this protocol include: (1) This PCR-based direct sequencing protocol generates information from markers of interest and provides a more streamlined and accurate analysis process, by multiplexing hundreds of informative markers into a single sequencing run. (2) The marker sets are easily customized to the species of interest and can readily be changed. In this study we have taken the GMS protocol developed in wheat and adapted it to barley. We have identified 577 SNP markers that work well using this protocol providing adequate genome coverage for genomic selection and tag 267 QTL's for genes of interest. Good markers have an adequate read depth of at least 5 amplicons and are reliably present across the population. [ABSTRACT FROM AUTHOR]

Plant breeding for the generation of cultivars adapted to local conditions has been an important and strategic concern of developing countries with agriculture-based economies. Considering economic constraints, breeders must improve genetic gain to increase the delivery of better cultivars with lower costs, through the implementation of molecular breeding and rapid generation advance. The aim of this work is to assess the actual economic impact of the implementation of these technologies on genetic gain for yield, rice blast disease resistance, and grain amylose content in a conventional rice breeding program. This analysis is intended as a case study of public breeding programs in developing countries. To accomplish this objective, cost analyses and genetic gain estimations were performed for four rice breeding scenarios: conventional and marker-assisted selection, with and without rapid generation advance. These estimations were then used to develop a cost index reflecting the breeding efficiency. The most efficient method was found to depend on the objective trait considered. For yield, there are small variations in genetic gain, but in terms of costs, the application of technology increases the breeding efficiency. For rice blast resistance, marker-assisted selection is not an efficient option when not using rapid generation advance. Conversely, the efficiency of marker-assisted selection increases when using rapid generation advance. For grain amylose content, the greatest effect on genetic gain is obtained when using marker-assisted selection. Rapid generation advance always increases the breeding efficiency. The use of new technological tools is recommended in terms of the cost–benefit function. [ABSTRACT FROM AUTHOR]

Rice is the most important staple food crop, and it feeds more than half of the world population. Brown planthopper (BPH) is a major insect pest of rice that causes 20–80% yield loss through direct and indirect damage. The identification and use of BPH resistance genes can efficiently manage BPH. A molecular marker-based genetic analysis of BPH resistance was carried out using 101 BC1F5 mapping population derived from a cross between a BPH-resistant indica variety Khazar and an elite BPH-susceptible line Huang–Huan–Zhan. The genetic analysis indicated the existence of Mendelian segregation for BPH resistance. A total of 702 high-quality polymorphic single nucleotide polymorphism (SNP) markers, genotypic data, and precisely estimated BPH scores were used for molecular mapping, which resulted in the identification of the BPH38(t) locus on the long arm of chromosome 1 between SNP markers 693,369 and id 10,112,165 of 496.2 kb in size with LOD of 20.53 and phenotypic variation explained of 35.91%. A total of 71 candidate genes were predicted in the detected locus. Among these candidate genes, LOC_Os01g37260 was found to belong to the FBXL class of F-box protein possessing the LRR domain, which is reported to be involved in biotic stress resistance. Furthermore, background analysis and phenotypic selection resulted in the identification of introgression lines (ILs) possessing at least 90% recurrent parent genome recovery and showing superior performance for several agro-morphological traits. The BPH resistance locus and ILs identified in the present study will be useful in marker-assisted BPH resistance breeding programs. [ABSTRACT FROM AUTHOR]

Arabinoxylans (AX) are major polymers of wheat grain cell walls and affect the end-use properties and nutritional quality. Total (TOT-AX), water-unextractable (WU-AX), and water-extractable (WE-AX) AX contents were determined in grain of 240 recombinant inbred wheat lines (RILs), derived from the cross PH82-2/Neixiang 188. A total of 195 SSR and STS markers were used to construct a genetic map and to detect quantitative trait loci (QTL). Wide ranges of variation in TOT-AX, WU-AX, and WE-AX contents were observed among the RILs, with line effects contributing the largest phenotypic variation. Broad sense heritabilities ( h) were 0.50, 0.38 and 0.71, respectively. Inclusive composite interval mapping (ICIM) identified four additive QTL for TOT-AX content on chromosomes 1B, 1D, 3B and 5B, explaining 3.7-14.6 % of the phenotypic variance (PV), among which two were involved in significant additive × season interactions, contributing 0.5-2.4 % of the PV. Two additive QTL for WU-AX content were identified on chromosomes 1B and 1D, accounting for 6.4 and 8.6 % of the PV, respectively; both were involved in significant additive × season interactions, contributing 0.6-1.4 % of the PV. Nine additive QTL for WE-AX content were identified on chromosomes 1A, 1B, 2B, 3B, 5A, 5B, 6B, 7A and 7B, explaining 3.8-15.2 % of the PV, and three of them were involved in significant additive × season interactions, contributing 0.5-2.1 % of the PV. Two pairs of epistatic QTL, with significant epistatic × season interactions, were identified for TOT-AX and WU-AX contents, contributing 16.6 and 18.6 % of the PV, respectively. The QTL identified on chromosomes 1B (associated with rye secalin marker sec1), 5A, 5B and 7A showed stable effects on WE-AX content across seasons. [ABSTRACT FROM AUTHOR]

Heavy metal (HM) toxicity is a considerable challenge that the current agricultural production systems and human population face worldwide. Among the HMs with pronounced toxic effects, cadmium (Cd) potentially contaminates a range of vital agricultural resources including soil and water together with severely impacting crop performance. Besides, gradual accumulation of Cd in food chain poses a global threat to food safety and environmental sustainability. Plants are equipped with meticulously orchestrated physiological and molecular mechanisms to respond and acclimatize to Cd-challenged scenarios. However, limited understanding about the HM toxicity mechanism involving metal uptake/transport, associated candidate gene (s) or QTLs and signaling crosstalk has greatly constrained breeding capacities to improve plants for HM tolerance. In the context, quantifying genetic variation for Cd tolerance accompanied by appropriate breeding schemes allowing the most efficient utilization of the estimated variation should be essentially undertaken. Concurrently, efforts are needed to facilitate fast-track introgression of genomic segments harboring candidate gene(s)/QTL for Cd tolerance to high yielding yet Cd-susceptible backgrounds. Advances in plant molecular biology have introduced refined techniques and methods to pinpoint genetic factors describing plant Cd tolerance. Ancillary to conventional breeding and marker assisted selection methods are modern transgenic technologies that offer attractive means to precisely interrogate the relevant molecular networks and manipulate the key Cd-related genes in plants. [ABSTRACT FROM AUTHOR]

Grain quality is an important feature of the marketing strategies of the rice industry in both domestic and international markets as quality influences the market price. With the demand for aromatic rice increasing steadily, export of short grain aromatic rices having premium grain quality is a viable option as the cultivation of basmati rices is limited to a specific geographic region. However, these native premium native aromatic rices require significant improvements in yield, plant stature and response to fertilizer and as grain quality traits are complex, their retention in the recombinants is a major challenge. With the recent advances in molecular markers, selection of recombinants with desirable traits is feasible through precise tracking of the target traits. The present study reports the successful recovery of the premium grain quality traits of Dubraj in IET 21044 (L9), a derivative from Pusa 44/Dubraj cross combination using pedigree approach employing markers associated with plant stature, aroma and grain quality and stringent phenotypic selection. The validation of the superior yield potential and premium grain quality of IET 21044 in the multi location evaluation trials over a 4 year period resulted in its release thus making it the first semi dwarf, high yielding, short grain aromatic rice released in India at the national level. The study was a successful demonstration of the limitless potential of the marker technology in breeding specialty rices. [ABSTRACT FROM AUTHOR]

During rice cultivation, brown planthopper (BPH, Nilaparvata lugens Stal.) and white-backed planthopper (WBPH, Sogatella furcifera) infestations cause decreased yield and rice quality. In this study, we attempted to develop multi-resistance plants and increase the marker-assisted selection (MAS) efficiency. The frequency of callus induction in 95 F doubled haploid lines (DHLs) derived from JSNDH13 (BPH resistance)/CNDH32 (WBPH resistance) ranged from 3.8 to 15.2 %. The plant regeneration rates varied from 2.9 to 39.3 %. Selected 75 DH plants were used to compare the results of WBPH bioassay and DNA marker reaction. The DHL bioassay showed continuous gene distribution and resistance score ranged from 0.5 to 9.0 (mean, 4.2). The broad-sense heritability for WBPH resistance was 51.7 %. The DHLs from the cross of JSNDH13/CNDH32 were segregated into 39 resistant (R):36 susceptible (S) to WBPH, i.e., 1 RR:SS. For the bioassay and MAS, RM11669 with WBPH resistance was selected. Genetically, the use of resistant cultivars, MAS, and DH breeding has proven to be environment friendly, efficient, and economical. This study confirmed the genetic basis for MAS to improve WBPH resistance in DHLs of WBPH/BPH resistant rice plants. [ABSTRACT FROM AUTHOR]

BS20-T is a thermo-sensitive genic male sterile (TGMS) wheat line ( Triticum aestivum L.) used in hybrid wheat breeding in northern China. BS20-T was crossed with common wheat variety ZN7. F plants were highly fertile. The segregation ratio of male fertile and male sterile individuals in F and BCF plants were close to 3:1 and 1:1, respectively. Other crosses of BS20-T also segregated for a single gene. Bulked sergeant analysis with SSR markers indicated the sterility gene was located on chromosome 2BL. It was named tmsBS20T. Screening of 162 extremely sterile and 30 extremely fertile F plants with linked markers indicated flanking by gwm403 and gwm374 with genetic distances of 2.2 and 4.5 cM, respectively. tmsBS20T was transferred into several common wheat varieties by using traditional hybridization combined with marker assisted selection with these two markers. Further identification of derived TGMS lines is ongoing. [ABSTRACT FROM AUTHOR]

Marker assisted backcrossing breeding has become one of the essential tools in transferring novel genes to adapted varieties and was employed to pyramid three blast resistance genes Pi1, Pi2 and Pi33 to a popular susceptible rice variety ADT43. Gene pyramiding process was facilitated by marker aided selection for both foreground as well as background genotype. Previously reported linked molecular markers were deployed to survey resistant and susceptible genotypes. In the BCF generation four lines viz, AC-B3-11-7, AC-B3-11-36, AC-B3-11-57, AC-B3-11-83 were identified to be pyramided with three genes and subjected to background analysis and a genome recovery up to 95 % was observed and advanced to further generations. Morphological, yield and grain quality traits were significantly similar to ADT43. The introgressed lines with three gene combinations were highly resistant to the blast pathogen compared to genotypes with single genes and the susceptible checks under blast nursery screening at two epiphytotic locations; Coimbatore and Gudalur. The selected three gene pyramided backcross lines in the desirable background were advanced to obtain an improved ADT 43 with resistance to blast disease. [ABSTRACT FROM AUTHOR]

Stripe rust resistance gene YrC591, present in wheat cultivar C591, is effective against currently important Puccinia striiformis Westend. f. sp. tritici isolates in China. An F population (127 lines) was developed by crossing C591 with susceptible cultivar Taichung 29. Thirty four simple sequence repeat (SSR) and 155 sequence tagged site (STS) markers located on chromosome 7BL were used to perform bulk segregant analysis. Eight SSR markers, cfa2040, wmc273, wmc166, gwm984, barc32 wmc276, barc182 and gwm146, and 6 STS markers, mag1714, mag1757, mag1811, BE425120, BE471173 and BG607810, were polymorphic between the parents and contrasting resistant and susceptible DNA pools. F lines were genotyped with these polymorphic markers. Linkage analysis indicated that YrC591 was flanked by Xmag1714 and Xbarc182 with genetic distances of 1.2 and 0.4 cM, respectively. In addition, validation of the SSR markers cfa2040, wmc273 and barc32, and STS markers mag1714 and BE425120 was carried out using wheat lines with C591 as a parent, indicating that these markers should be effective in tracing this gene in marker-assisted selection. [ABSTRACT FROM AUTHOR]

Phytohormones, a group of structurally unrelated small molecules are plant-signalling compounds that trigger induced resistance against certain pathogens and herbivores. The hormones jasmonic acid (JA), ABA, salicilic acid (SA) and ethylene (ET) are known to play major roles in regulating plant defence responses. In order to determine the changes in growth and in the chlorophyll content induced by the exogenous application of these elicitors, a set of DH lines of the Oregon-Wolfe Barley mapping population, previously screened to locate aphid resistant genes, was investigated. The aim of the current research was to map the induced defence genes and to reveal the relationship with aphid resistance. There were highly significant differences between controls and hormone treated plants in the aerial fresh and dry weights (AFW, ADW), the foliar area (FA) and the root dry weight (RDW). More than 15 JA and ET-induced lines exceeded the chlorophyll (Ch) values of their controls. Most of the plant traits were associated with the same genetic windows on chromosomes 3H, 5H and 7H in the controls and hormone treated plants. QTL(s) identified on chromosome 3H and 5H explained most of the variation of AFW, ADW, FA and RDW of controls and treated plants. QTL(s) located on chromosome 5H were associated with the variation of chlorophyll contents on JA-treated plants. The Ch in ET and ABA-treated plants was associated with two different regions on chromosome 7H. One of the latter genetic windows also explained the variation of RDW of ET- and ABA-treated plants. A sequence homology search was performed to derive the putative function of the genes linked to the QTLs. Several QTLs were identified located close to aphid resistance genes previously mapped. This is the first report of genes associated with hormone response in barley that could be involved with insect resistance. Those recombinant lines carrying the appropriate alleles could be useful for breeding barley to enlarge the genetic base of defence against stress. [ABSTRACT FROM AUTHOR]

Gelatinization temperature and apparent amylose content are key parameters used to describe the eating and cooking qualities of rice. Sequence variants of SSIIa and Waxy genes are important determinants of gelatinization temperature and apparent amylose content, respectively. A collection of Italian non-glutinous japonica rice accessions was characterized for sequence polymorphisms in SSIIa and Waxy genes, in comparison with non-Italian japonica and indica genotypes. For SSIIa two markers, SNP3 and SNP4, were used. A PCR amplification of multiple specific alleles protocol was developed for the identification of G/T polymorphism in 5′ splice site of first intron and A/C polymorphism in exon 6 of the Waxy gene. Based on simple allele-specific PCR, it can be proposed as a user-friendly, cost-effective tool for marker-assisted selection of amylose content. The collection was characterized also for the (CT)n repeats in exon 1 of the Waxy gene. The results showed that while SSIIa haplotypes were rather similar between Italian and non-Italian japonica rice, the Waxy gene haplotype T/A/(CT)18 was largely predominant in Italian accessions, other haplotypes, well represented in non-Italian japonica [T/A/(CT)19] and indica [e.g. G/C/(CT)20] genotypes, were present at lower frequency. Grain starch quality traits as apparent amylose content and RVA profile were also analysed. The In1/Ex6 SNP haplotypes of Wx gene were found to explain 79 % of variation in apparent amylose content, and 36, 22 and 25 %, of variation in the RVA parameters peak viscosity, breakdown and setback, respectively. The additional use of (CT)n repeats marker further improved the association of haplotypes with RVA parameters. [ABSTRACT FROM AUTHOR]

The evaluation and use of the vast diversity contained in plant genetic resources (PGR) is a main challenge for today's plant breeding. The use of molecular markers has hugely increased the knowledge about genetic diversity and great hopes are raised about the potential of marker assisted selection [MAS; sometimes also termed SMART breeding (Selection with Markers and Advanced Reproductive Technologies)] to help increasing the use of PGR and maintaining crop genetic diversity. Another approach growing attention has been paid to over the past two decades and which also aims to increase variation in crops is evolutionary and participatory breeding (EPB). In this paper we discuss both the potential of marker-assisted breeding strategies and the potential of EPB breeding to contribute to the maintenance, increase and development of agrobiodiversity. The potentials of molecular markers in the evaluation and use of PGR and their documented contribution to agrobiodiversity are reviewed and results from guided interviews with scientists and breeders are given. Despite tremendous research efforts involving molecular markers, it is still difficult to obtain a clear picture how molecular markers contribute to the use of PGR in plant breeding. Minor and major crops do not benefit to the same degree from recent developments in marker technology. It therefore depends at least in part on economic considerations whether SMART breeding or EPB strategies or both are implemented in the breeding process of a crop. A general decision in favor or against MAS or EPB when breeding for diversity would not yield optimum results. [ABSTRACT FROM AUTHOR]

The association between high malting quality and pre-harvest sprouting (PHS) susceptibility is a key challenge when developing new malting barley varieties. A new malting barley variety Baudin has successfully combined high malting quality and PHS tolerance. A doubled haploid population was developed for mapping PHS tolerance and seed dormancy from a cross of Baudin × AC Metcalfe using 233 molecular markers. Three QTLs were mapped for seed dormancy based on the standard germination test at 24, 48 and 72 h. One major QTL was mapped to the long arm of chromosome 5H controlling seed dormancy and PHS tolerance from Baudin. Two other minor QTLs were identified from Baudin on chromosomes 3 and 7H. QTL/QTL interaction was detected for seed dormancy between chromosomes 3 and 5H. The PHS tolerance allele of the 5H QTL from Baudin contributes to higher malt yield without significant impact on diastatic power, beta-glucan content and wort viscosity. QTL from Baudin provide new sources to integrate PHS tolerance and high malting quality. [ABSTRACT FROM AUTHOR]

Phenotypic and genetic evaluation of morphological traits associated with herbage biomass production was undertaken in a perennial ryegrass ( Lolium perenne L.) biparental F mapping population ( n = 200) with parent plants from cultivars 'Grasslands Impact' and 'Grasslands Samson'. Morphological traits measured on three clonal replicates of the parental genotypes and 200 F progeny in a glasshouse in two separate trials (autumn and spring) included: dry weight (DW), leaf elongation rate (LER), initial tiller number (TNs), final tiller number (TNe), site filling (Fs), tiller weight (TW), leaf lamina length, leaf tip and ligule appearance rates (ALf, ALg) and leaf elongation duration (LED). Principal component analysis of patterns of trait association identified negative correlation between TNs or TNe, and TW as the primary basis for morphological difference and indicated that either high LER or long LED could reduce TN. Plants with higher LER tended to have increased DW. Quantitative trait loci (QTL) were detected on all seven linkage groups (LG) of a perennial ryegrass linkage map for all but three traits. A total of 61 QTL were identified, many of which clustered at 15 shared genome locations. Significant genotype by environment effects were encountered, evidenced both by variation between experiments in genotype rankings and by a general lack of commonality for QTL for the same traits in the different experiments. Only five QTL, for ALf, ALg and TN, were conserved between autumn and spring trials. A QTL for TN and DW on LG6 is a strong candidate for application of MAS in future plant improvement work and was found to be co-linear with QTL for equivalent traits reported on chromosome 2 in rice. [ABSTRACT FROM AUTHOR]

Heat stress adversely affects wheat production in many regions of the world and is particularly detrimental during reproductive development. The objective of this study was to identify novel quantitative trait loci (QTL) associated with improved heat tolerance in wheat ( Triticum aestivum L.) and to confirm previous QTL results. To accomplish this, a recombinant inbred line (RIL) population was subjected to a three-day 38°C daytime heat stress treatment during early grain-filling. At maturity, a heat susceptibility index (HSI) was calculated from the reduction of three main spike yield components; kernel number, total kernel weight, and single kernel weight. The HSI, as well as temperature depression (TD) of the main spike and main flag leaf during heat stress were used as phenotypic measures of heat tolerance. QTL analysis identified 14 QTL for HSI, with individual QTL explaining from 4.5 to 19.3% of the phenotypic variance. Seven of these QTL co-localized for both TD and HSI. At all seven loci, the allele for a cooler flag leaf or spike temperature (up to 0.81°C) was associated with greater heat tolerance, indicated by a lower HSI. In a comparison to previous QTL results in a RIL population utilizing the same source of heat tolerance, seven genome regions for heat tolerance were consistently detected across populations. The genetic effect of combining three of these QTL, located on chromosomes 1B, 5A, and 6D, demonstrate the potential benefit of selecting for multiple heat tolerance alleles simultaneously. The genome regions identified in this study serve as potential target regions for fine-mapping and development of molecular markers for more rapid development of heat tolerant germplasm. [ABSTRACT FROM AUTHOR]

traditional Type 3 Basmati rice cultivar grown in India is tall and lodges even under low nitrogen fertilizer dose. In addition to lodging, it is highly susceptible to several diseases and pests including bacterial blight (BB). BB resistance genes ( Xa21 and xa13) and a semidwarfing gene ( sd- 1) were pyramided in Type 3 Basmati from a rice cultivar PR106-P2 using marker-assisted selection (MAS). Foreground selection for BB resistance genes, Xa21 and xa13 and reduced plant height gene, sd- 1 was carried on the basis of linked molecular markers pTA248, RG136 and 'h', respectively. The BCF progenies with both the BB resistance genes were highly resistant with lower lesion length than either of the genes individually. Background profiling of the selected 16 BCF progenies was done using 95 anchored SSR and 12 ISSR markers. Among the selected 16 BCF progenies, 38-5-2 and 38-5-36 closely clustered along with the recipient parent Type 3 Basmati showing above 85% genetic similarity with the same. Further selection was continued till F generation for higher recovery for Type 3 Basmati characteristics. The desirable alleles of intermediate amylose content ( wx) and aroma ( fgr) loci of Type 3 Basmati were also tracked using the linked SSR markers. The BCF pyramid lines T3-4, T3-5, T3-6 and T3-7 homozygous for the three target genes Xa21, xa13 and sd- 1 from the donor parent with wx and fgr alleles of Type 3 Basmati had excellent cooking quality and strong aroma. [ABSTRACT FROM AUTHOR]

In this study, a F population derived from the cross between deep-rooted variety 'Moroberekan' with shallow-rooted variety 'IR20' were used to identify and validate of SSR markers associated with root morphological traits. The F lines were divided into two groups. In the first group, 152 seedling having minimum of four tillers were chosen and separated into four plantlets to plant them in polyvinyl chloride pipes for root study under well-watered (WW) condition at maturity stage. The lines were genotyped using SSR markers. QTLs for maximum root length (MRL) and root dry weight showed co-segregation with RM472, RM7 and RM201. The same material was forwarded to next generation (F) to validate the linked markers under both WW and low-moisture stress (LMS) conditions. These three markers were associated consistently with MRL across generations. In the second group, 1240 F plants were forwarded to F using SSD breeding method to test the effectiveness of the marker-assisted selection (MAS) method for drought resistant. The high performing genotypic group was significantly superior to low performing genotypic group for MRL, grain yield, root volume, root dry weight and root number, indicating the efficiency of MAS for root-related traits under LMS. Comparing MAS with farmer selection in F, the results showed that MAS group means were significantly different from farmer group means for MRL, root volume, root dry weight and root number. Thus, MAS was combined with participatory selection to select five high-yielding and deep rooted promising lines. Identification of stable QTL for root morphological traits under WW and LMS conditions can aid in MAS and to introduce them into varieties with good yield potential and accepted by farmer. [ABSTRACT FROM AUTHOR]

Squash silverleaf (SSL), caused by the silverleaf whitefly [ Bemisia argentifolii (formerly known as Bemisia tabaci Gennadius, B strain)], is an important physiological disorder that affects squash ( Cucurbita spp.) by reducing yield potential. Breeding squash with resistance to SSL disorder can be facilitated by using marker-assisted selection (MAS). Resistance to SSL disorder, in Cucurbita pepo, is conferred by a single recessive gene ( sl). The objective of this study was to identify molecular markers associated with resistance. A zucchini squash, SSL disorder resistant breeding line, ‘Zuc76’ ( sl/ sl) and a SSL disorder susceptible zucchini cultivar ‘Black Beauty’ ( Sl/ Sl) were screened with 1,152 randomly amplified polymorphic DNA (RAPD) primers and 432 simple sequence repeat (SSR) markers to identify polymorphisms. Using F2 and BC1 progeny segregating for SSL disorder resistance, three RAPD (OPC07, OPL07 and OPBC16) primers and one SSR (M121) marker were found associated with sl. Fragments amplified by RAPD primer OPC07 was linked in coupling phase to sl, whereas RAPD primer OPL07 was linked in repulsion phase. RAPD primer OPBC16 and SSR marker M121 were co-dominant. The allelic order of these loci was found to be M121– sl–OPC07–OPL07–OPBC16. The closest marker to sl is M121 with an estimated genetic distance of 3.3 cM. The markers identified in this study will be useful for breeding summer squash ( C. pepo) for SSL disorder resistance derived from zucchini squash breeding line ‘Zuc76’. [ABSTRACT FROM AUTHOR]

The frequency of soybean white mold ( Sclerotinia sclerotiorum, SWM) outbreaks has increased since 1978, and this disease is currently considered to be the second most important cause of soybean yield loss worldwide. We have studied SWM in stems of soybean cultivar Maple Arrow, which shows partial resistance to SWM, in an attempt to identify the quantitative trait loci (QTLs) underlying soluble pigment(s) content, which is associated with SWM resistance. A SWM-susceptible cultivar, Hefeng 25, was crossed with Maple Arrow, and 149 F5:6 recombinant inbred lines were subsequently advanced through single-seed-descent. A total of 109 simple sequence repeat (SSR) markers were used to construct a genetic linkage map. Three QTLs for soluble pigment content in soybean stems associated with the resistance to SWM, namely, Qsp-1 (Satt502-Sat_159), Qsp-2 (Sat_156-Satt251), and Qsp-3 (Satt525-Satt233), were identified in 2007 and 2008 and located onto linkage groups D1a+q, B1 and A2, respectively. The phenotypic variation ( R2) explained by these QTLs ranged from 6.29 to 15.37%. These three QTLs were not significantly related to known QTLs associated with escape resistant mechanisms. The use of these QTLs in marker-assisted selection may contribute to improved soybean resistance to SWM. [ABSTRACT FROM AUTHOR]

Two cucumber recombinant inbred lines (RILs) differing in plant habit were crossed and progeny self-pollinated to produce F3 individuals upon which phenotypic selection was practiced to identify a base population which in turn underwent either two cycles of MAS or random mating without selection (RAN). MAS and RAN were practiced to produce F4 and F5 progeny sets. RIL, crossing parents, and F3–F5 progeny sets were then evaluated under replicated field conditions for fruit yield and quality (L:D and E:T) to evaluate gain from selection (ΔG). The broad-sense heritability ( h 2 B) over cycles (C) of selection ranged 0.22–0.45, 0.09–0.20, and 0.11–0.15 for yield, L:D, and E:T, respectively. Although one cycle of PHE selection followed by MAS was effective in conserving the performance of the traits examined during inbreeding, progeny performance during RAN fluctuated (F4–F5 generation; C2). Lack of ΔG during advanced generations (F4–F5) of MAS was likely due to allelic fixation and/or optimized epistatic complementation. [ABSTRACT FROM AUTHOR]

The pol cytoplasmic male-sterility system has been widely used as a component for utilization of heterosis in Brassica napus and offers an attractive system for study on nuclear–mitochondrial interactions in plants. Genetic analyses have indicated that one dominant gene, Rfp, was required to achieve complete fertility restoration. As a first step toward cloning of this restorer gene, we attempted molecular mapping of the Rfp locus using the amplified fragment length polymorphism (AFLP) technique combined with bulked segregant analysis (BSA) method. A BC1 population segregating for Rfp gene was used for tagging. From the survey of 1,024 AFLP primer combinations, 13 linked AFLP markers were obtained and five of them were successfully converted into sequence characterized amplified region (SCAR) markers. A population of 193 plants was screened using these markers and the closest AFLP markers flanking Rfp were at the distances of 2.0 and 5.3 cM away, respectively. Further the AFLP or SCAR markers linked to the Rfp gene were integrated to one doubled-haploid (DH) population derived from the cross Quantum × No.2127-17 available in our laboratory, and Rfp gene was mapped on N18, which was the same as the previous report. These molecular markers will facilitate the marker-assisted selection (MAS) of pol CMS restorer lines. [ABSTRACT FROM AUTHOR]

In faba bean, field based winter-hardiness is a complex trait that is significantly correlated to frost tolerance. Frost tolerance could be used to indirectly select for faba bean winter-hardiness. The aim of this study was to identify putative QTL associated with frost tolerance and auxiliary traits and to quantify the efficiency of marker assisted selection. Thus, 101 recombinant inbred lines derived from the cross between two frost tolerant lines were tested for their hardened and unhardened frost tolerance and for their leaf fatty acid content in both treatments. Significant differences among the RIL were observed for all studied traits. For frost tolerance, five putative QTL were detected; three for unhardened frost tolerance that explained 40.7% (8.6% after cross-validation, CV) of its genotypic variance and two for hardened frost tolerance that explained 21.8% (1.0% after CV). For fatty acid content, three QTL were detected for oleic acid content in unhardened leaves that explained 62.9% (40.6% after CV) of its genotypic variance. This fatty acid was significantly correlated with unhardened frost tolerance. The unbiased genotypic variance explained enabled to draw realistic prospects of MAS for frost tolerance. In this study, combined MAS was more efficient than classical phenotypic selection and was expected to be higher on larger populations at early generations. Moreover, favourable alleles inherited from the exotic line BPL 4628 could be introgressed to European winter-hardy beans for further improvement. [ABSTRACT FROM AUTHOR]

Soybean ( Glycine max L. Merr.) pod borer ( Leguminivora glycinivorella (Mats.) Obraztsov) (SPB) results in severe loss in soybean yield and quality in certain regions of the world, especially in Northeastern China, Japan and Russia. The aim here was to evaluate the inheritance of pod borer resistance and to identify quantitative trait loci (QTL) underlying SPB resistance for the acceleration of the control of this pest. Used were the 129 recombinant inbred lines (RILs) of the F5:6 derived population from ‘Dong Nong 1068’ × ‘Dong Nong 8004’ and 131 SSR markers. Correlations between the percentage of damaged seeds (PDS) by pod borer and plant, pod and seed traits that were potentially related to SPB resistance were analyzed. The results showed highly significant correlations between PDS by pod borer and plant height (PH), maturity date (MA), pod color (PC), pubescence density (PB), 100-seed weight (SW) and protein content existed. Soybeans with dwarf stem, light color of pod coat, small seeds, lower density of pubescence, early maturity and low content of protein seemed to have higher resistance to SPB. The correlated traits had potential to inhibit egg deposition and thereby to decrease the damage by SPB. Three QTL directly associated with the resistance to SPB judged by PDS at harvest were identified. qRspb-1 (Satt541–Satt253) and qRspb-2 (Satt253–Satt314) were both on linkage group (LG) H and qRspb-3 (Satt288–Satt199) on LG G. The three QTL explained 10.96, 9.73 and 11.59% of the phenotypic variation for PDS, respectively. In addition, 12 QTL that underlay 10 of 13 traits potentially related with SPB resistance were found. These QTL detected jointly provide potential for marker assisted selection to improve cultivar resistance to SPB. [ABSTRACT FROM AUTHOR]

The powdery mildew resistance gene Pm6, transferred to common wheat from the tetraploid Triticum timopheevii, is effective in most epidemic areas for powdery mildew in China. RFLP probe BCD135 was previously associated with Pm6. In the present research, four STS primers (NAU/STSBCD135-1, NAU/STSBCD135-2, STS003 and STS004) were designed from the sequence data of BCD135. These primers were used for PCR amplification using the genomic DNA of resistant near-isogenic lines with Pm6 and their recurrent parent, cv. Prins. No polymorphic product was observed using primers STS003 and STS004; however, primers NAU/STSBCD135-1 and NAU/STSBCD135-2 amplified two and one bands, respectively, polymorphic between the resistant near-isogenic-lines and Prins. The two primers were then used to amplify the F2 population from the cross IGV1-465 (FAO163b/7*Prins) × Prins. The amplification and the powdery mildew resistance identification data were analyzed using the software Mapmaker 3.0. The results indicated that both NAU/STSBCD135-1 and NAU/STSBCD135-2 were closely linked to Pm6 with a genetic distance of 0.8 cM. A total of 175 commercial varieties without Pm6 from different ecological areas of China were tested using marker NAU/STSBCD135-2 and none of them amplified the 230 bp-specific band. This marker thus has high practicability and can be used in MAS of Pm6 in wheat breeding programs for powdery mildew resistance. [ABSTRACT FROM AUTHOR]

Rs1046AB is a line which is true breeding for a dominant genetic male sterility gene ( Ms) but which is a mixture of male fertile and sterile individuals (a two-type line) because it is segregating for a dominant suppressor gene ( Rf). This system provides a promising alternative to the CMS system for hybrid breeding in Brassica napus. In order to identify molecular markers linked to the rf gene, a near-isogenic line (NIL) population from the cross between a sterile individual ( MsMsrfrf) and a fertile individual ( MsMsRfrf) in Rs1046AB was subjected to amplified fragment length polymorphism (AFLP) analysis, with a combination of comparing near isogenic lines (NILs) and bulked segregant analysis (BSA). From 2,816 pairs of AFLP primers, six fragments showing polymorphism between the fertile and sterile bulks as well as the individuals of the bulks were identified. Linkage analysis indicated that the six AFLP markers are tightly linked to the Rf gene and all are distributed on the same side. The minimum genetic distance between the Rf gene and a marker was 0.7 cM. Since the AFLP markers are not suitable for large-scale application in MAS (marker-assisted selection), our objective was to develop a fast, cheap and reliable PCR-based assay. Consequently, three of the four closest AFLP markers were converted directly to sequence characterized amplified region (SCAR) markers. For the other marker a corresponding SCAR marker was successfully obtained after isolating the adjacent sequences by PCR Walking. The available SCAR markers of the Rf gene will greatly facilitate future breeding programs using dominant GMS to produce hybrid varieties. [ABSTRACT FROM AUTHOR]

We have previously identified 2 RAPD and 8 AFLP markers that were associated with yellow seed coat gene in a stable and pure yellow-seeded DH line No. 2127-17, however, they were not suitable in large-scale MAS. In this paper, it reported our efforts in developing rapid and reliable SCAR and CAPS markers from the RAPD and AFLP markers. Based on the sequence information in the regions of the most closely linked 4 AFLP and 2 RAPD markers, one SCAR (SCS1130) and one CAPS (SCA1) maker were successfully developed. Linkage analysis on a 127 DH lines population derived from the cross Hui5148-2 × No. 2127-17 revealed that they were tightly flanked (3.2 cM, 3.8 cM respectively). The resulting SCS1130 and SCA1 were further evaluated in backcross breeding families and demonstrated more accurate and valuable in MAS breeding. The development of these new markers would facilitate and accelerate the yellow seed coat breeding in Brassica napus. [ABSTRACT FROM AUTHOR]

There is an increasing amount of public sequence information for the main cultivated cereals, such as wheat and barley. It is not foreseeable that comparable efforts or resources could be devoted to related wild species. However, wild species are interesting sources of genetic variation through introgression breeding. Comparative genomics can be a helpful approach to make use of the available genomic resources. In this context, the potential of the wild barley species Hordeum chilense has been explored in recent years. It exhibits great levels of polymorphism and high crossability with different cereal genera. In addition, interesting biotic and abiotic stress resistance genes, and important quality traits like carotene content and seed storage protein variability shown in the species are also expressed in wheat backgrounds, and are the basis of a breeding program. Different approaches have been undertaken for tagging H. chilense genomic regions in a wheat background. The search for the most suitable DNA marker system started with the development of RAPD and SCAR markers due to a lack of sequence information from the wild species. Transferability of markers from wheat and barley (like STSs or SSRs) have also been useful approximations. More recently, SNP development is being accomplished for the species. In this work, the situation and prospects with the available molecular tools are considered from a practical point of view. [ABSTRACT FROM AUTHOR]

Crown rust resistance is an important selection criterion in ryegrass breeding. The fungal disease caused by P. coronata causes yield loss and a reduced quality of the fodder crop. Molecular markers were used to unravel the genomic organization of crown rust resistance in a segregating L. perenne population. Two genomic regions involved in crown rust resistance were identified that together explained 35% of the phenotypic variance present. Bulked segregant analysis in combination with AFLP markers was a suitable method to identify DNA markers associated with genomic regions of major effect. One cluster of AFLP markers explained 6.1% of the variance and mapped to linkage group 2, a genomic region known to contain crown rust resistance genes. A second cluster of AFLP markers detected a novel genomic region of major effect that explained 27.7% of the phenotypic variance in crown rust resistance. This cluster was unlinked to the cluster on linkage group 2. Divergent selections performed within the segregating F1 population on the basis of genotype and phenotype revealed that the markers associated with crown rust resistance identified in this study have potential for marker assisted selection. Selection of plants on the basis of markers was more straightforward than the selection on the basis of phenotype. [ABSTRACT FROM AUTHOR]

Winter durum (Triticum turgidum var. durum) growing is favored in Germany, Austria, and Hungary. With the invasion of the aggressive Warrior race with a wider virulence spectrum of the yellow rust (YR) causing pathogen, YR came into focus of durum breeders. Accordingly, a local epidemic of stem rust in winter wheat 2013 gained much attention. Therefore, we aimed to analyze the genetic architecture of resistance to YR and stem rust (SR) in a diversity panel of 328 durum lines genotyped by 12,550 mapped markers. Infections were successful in three environments for YR and one environment for SR. Additionally, cumulative ratings of leaf and ear health were conducted in five and three environments, respectively. The genome-wide association analysis revealed six to eight quantitative trait loci (QTL) per trait with an explained total genotypic variance of 42% (YR) to 75% (ear health). Sequence comparison with a reference genome indicated that three YR (Yr10, Yr51, YrH9014) and two SR (Sr56, Sr8155B1) resistance genes might be present in the diversity panel. Other QTL with explained genotypic variances ranging from 1.5 to 21% were detected. The difference between marker-assisted selection and genomic prediction was the highest for those traits with lower explained genetic variance (YR, leaf health) indicating that an array of non-detected QTL was used for genomic prediction. Genomics-assisted breeding could greatly help in achieving complex resistances in cultivars. [ABSTRACT FROM AUTHOR]

Fruit spine size is one of the importantly external quality traits effected the economic value of cucumber fruit. Morphological-cytological observation of the fruit spine size phenotype indicated that large spine formation arises from an increasing of spiny pedestal cell number caused by cell division, and best periods to accurately score fruit spine size trait was 4th day before flowering to 7th day after flowering according the continuous observation. Genetic analysis showed that a single dominant gene determined the fruit spine size trait in cucumber. BC1 population (189 individuals) of two inbred lines (large spine PI197088 and small spine SA0422) was used for primary mapping of the SS/ss locus with 7 markers covering an interval of 37.1 cM. An F2 segregating population of 1032 individuals constructed from the same two parents (PI197088 and SA0422) was used to fine mapping of the SS/ss locus. Six new markers linked to the gene were successfully screened for construction of a fine linkage map, in which the SS/ss locus was located in the region flanked by marker SE1 (3 recombinants) and SSR43 (2 recombinants) with a 189 kb physical distance. Markers from this study will be valuable for candidate gene cloning and marker-assisted selection for cucumber breeding. [ABSTRACT FROM AUTHOR]