Allele-specific amplification for the detection of ascochyta blight resistance in chickpea

A new co-dominant molecular marker, CaETR, was developed based on allelic sequence length polymorphism in an ethylene receptor-like gene located in the genomic region of a QTL (QTL_AR1) conferring ascochyta blight resistance in chickpea. This marker not only discriminated resistance and susceptible phenotypes of chickpea to ascochyta blight, but also easily detected heterozygous genotypes. Using the CaETR marker in combination with a previously developed co-dominant SCAR marker (SCY17₅₉₀) linked to another QTL (QTL_AR2) it was possible to detect resistance alleles in 90?% of resistant accessions in a collection of landraces, advances breeding lines and cultivars, and also detected susceptible alleles in all cases. The results of this study offer a scope for improving the efficiency of conventional chickpea breeding by carrying out negative selection for QTL_AR1 and QTL_AR2 in early generations without relaying directly on the phenotype. This PCR-based approach using both co-dominant markers is proposed as an efficient tool for selecting blight-resistant genotypes in breeding programs.     

A segregation distortion locus located on linkage group 4 of the chickpea genetic map

A chickpea F₂ population of 593 plants derived from the intraspecific cross ILC3279 × WR315 was genotyped for markers closely linked to quantitative trait loci (QTLs) for ascochyta blight resistance (QTL_AR1 and QTL_AR2 located on linkage group 4 and QTL_AR3 on linkage group 2). All the markers located on linkage group 4 exhibited strongly distorted segregation with respect to the expected Mendelian inheritance, towards the male parental line. This skewed segregation was also observed in a second F₂ population of 50 plants derived from the same cross, confirming the presence of a region of distorted segregation on this linkage group and its heritability. The most skewed markers were SC-Y17 and TA72, which were tightly linked to each other, indicating that they may both be closely associated with the genetic factor responsible for segregation distortion in chickpea. To attempt to explain the non-Mendelian segregation, by identifying factors to which it could be attributed, three different chi-square tests were carried out to test different hypotheses using the data obtained from examining co-dominant markers associated with segregation distortion. According to our results, the distorted segregation could be caused by gametophytic factors that affect either male or female gametes. Pollen fertility and meiosis were also analysed to determine their relationship with segregation distortion; however, these not seem to be inducing factors in the non-Mendelian segregation reported in this study.     

Molecular mapping of QTLs for resistance to Fusarium wilt (race 1) and Ascochyta blight in chickpea (Cicer arietinum L.)

Fusarium wilt (FW) and Ascochyta blight (AB) are two important diseases of chickpea which cause 100 % yield losses under favorable conditions. With an objective to validate and/or to identify novel quantitative trait loci (QTLs) for resistance to race 1 of FW caused by Fusarium oxysporum f. sp. ciceris and AB caused by Ascochyta rabiei in chickpea, two new mapping populations (F_2:3) namely ‘C 214’ (FW susceptible) × ‘WR 315’ (FW resistant) and ‘C 214’ (AB susceptible) × ‘ILC 3279’ (AB resistant) were developed. After screening 371 SSR markers on parental lines and genotyping the mapping populations with polymorphic markers, two new genetic maps comprising 57 (C 214 × WR 315) and 58 (C 214 × ILC 3279) loci were developed. Analysis of genotyping data together with phenotyping data collected on mapping population for resistance to FW in field conditions identified two novel QTLs which explained 10.4–18.8 % of phenotypic variation. Similarly, analysis of phenotyping data for resistance to seedling resistance and adult plant resistance for AB under controlled and field conditions together with genotyping data identified a total of 6 QTLs explaining up to 31.9 % of phenotypic variation. One major QTL, explaining 31.9 % phenotypic variation for AB resistance was identified in both field and controlled conditions and was also reported from different resistant lines in many earlier studies. This major QTL for AB resistance and two novel QTLs identified for FW resistance are the most promising QTLs for molecular breeding separately or pyramiding for resistance to FW and AB for chickpea improvement.     

Further QTL mapping for yield component traits using introgression lines in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) under drought field environments

To better understand the underlying mechanisms of agronomic traits related to drought resistance and discover candidate genes or chromosome segments for drought-tolerant rice breeding, a fundamental introgression population, BC₃, derived from the backcross of local upland rice cv. Haogelao (donor parent) and super yield lowland rice cv. Shennong265 (recurrent parent) had been constructed before 2006. Previous quantitative trait locus (QTL) mapping results using 180 and 94 BC₃F_6,7 rice introgression lines (ILs) with 187 and 130 simple sequence repeat (SSR) markers for agronomy and physiology traits under drought in the field have been reported in 2009 and 2012, respectively. In this report, we conducted further QTL mapping for grain yield component traits under water-stressed (WS) and well-watered (WW) field conditions during 3 years (2012, 2013 and 2014). We used 62 SSR markers, 41 of which were newly screened, and 492 BC₄F_2,4 core lines derived from the fourth backcross between D123, an elite drought-tolerant IL (BC₃F₇), and Shennong265. Under WS conditions, a total of 19 QTLs were detected, all of which were associated with the new SSRs. Each QTL was only identified in 1 year and one site except for qPL-12-1 and qPL-5, which additively increased panicle length under drought stress. qPL-12-1 was detected in 2013 between new marker RM1337 and old marker RM3455 (34.39 cM) and was a major QTL with high reliability and 15.36% phenotypic variance. qPL-5 was a minor QTL detected in 2013 and 2014 between new marker RM5693 and old marker RM3476. Two QTLs for plant height (qPHL-3-1 and qPHP-12) were detected under both WS and WW conditions in 1 year and one site. qPHL-3-1, a major QTL from Shennong265 for decreasing plant height of leaf located on chromosome 3 between two new markers, explained 22.57% of phenotypic variation with high reliability under WS conditions. On the contrary, qPHP-12 was a minor QTL for increasing plant height of panicle from Haogelao on chromosome 12. Except for these two QTLs, all other 17 QTLs mapped under WS conditions were not mapped under WW conditions; thus, they were all related to drought tolerance. Thirteen QTLs mapped from Haogelao under WS conditions showed improved drought tolerance. However, a major QTL for delayed heading date from Shennong265, qDHD-12, enhanced drought tolerance, was located on chromosome 12 between new marker RM1337 and old marker RM3455 (11.11 cM), explained 21.84% of phenotypic variance and showed a negative additive effect (shortening delay days under WS compared with WW). Importantly, chromosome 12 was enriched with seven QTLs, five of which, including major qDHD-12, congregated near new marker RM1337. In addition, four of the seven QTLs improved drought resistance and were located between RM1337 and RM3455, including three minor QTLs from Haogelao for thousand kernel weight, tiller number and panicle length, respectively, and the major QTL qDHD-12 from Shennong265. These results strongly suggested that the newly screened RM1337 marker may be used for marker-assisted selection (MAS) in drought-tolerant rice breeding and that there is a pleiotropic gene or cluster of genes linked to drought tolerance. Another major QTL (qTKW-1-2) for increasing thousand kernel weight from Haogelao was also identified under WW conditions. These results are helpful for MAS in rice breeding and drought-resistant gene cloning.     

Genetic analysis and identification of QTLs for resistance to cucumber mosaic virus in chili pepper (Capsicum annuum L.)

A pepper (Capsicum annuum) inbred line ‘BJ0747-1-3-1-1’ was found to exhibit resistance to a cucumber mosaic virus (CMV) local isolate (CMV-HB). In order to exploit the genetic mechanism of CMV resistance in this pepper line, inheritance and genetic linkages of CMV resistance were studied. The CMV-resistant ‘BJ0747-1-3-1-1’ (P₁) was crossed to the susceptible line ‘XJ0630-2-1-2-1-1’ (P₂), and the F₂ and back-cross populations (B₁ and B₂) were generated for segregation analysis following a mixed inheritance model. Analysis of the segregation data revealed that CMV resistance in ‘BJ0747-1-3-1-1’ is controlled by two partially additive-dominant major genes and additive-dominant polygenes. Analysis of the results from two growth seasons also identified two stable and major QTLs for CMV resistance that collectively explained 55 % of the trait variation. One of the two major QTLs was found on linkage group 8 (LG8) between markers TS52 and HpmsE1-43, and accounted for 37.7–43.5 % of the variation in the two inoculation experiments. The other QTL on LG4 between markers UBC843 and S74 was found to be responsible for 10.7–11.2 % of the trait variation. QTLs with minor effects on CMV resistance were also identified. This work provides an example for genetic analysis and QTL mapping of other disease-resistance genes in pepper and the findings should be useful for molecular marker-assisted breeding programs that aim at developing disease-resistant cultivars in peppers.     

Genetic mapping of gummy stem blight (Didymella bryoniae) resistance genes in Cucumis sativus-hystrix introgression lines

Gummy stem blight (GSB, Didymella bryoniae (Auersw.) Rehm) is a devastating disease occurring worldwide in cucumber (Cucumis sativus L.) production and causing considerable yield loss. No commercially available cultivars are resistant to GSB. By screening 52 introgression lines (ILs) derived from the cross of C. hystrix × C. sativus and eight cucumber cultivar/lines through a whole plant assay, three ILs (HH1-8-1-2, HH1-8-5, HH1-8-1-16) were identified as GSB resistant lines. Six common introgression regions in these three ILs were on Chromosomes 1, 4, and 6. To further map the resistance in the ILs, three mapping populations (2009F₂, 2009F₂′ and 2010F₂) from a cross between resistant IL HH1-8-1-2 and susceptible 8419 were constructed and used for QTL mapping with SSR markers. Two quantitative trait loci (QTLs) were identified; one on Chromosome 4 and the other on Chromosome 6. The interval for Chromosome 4 QTL is 12 cM spanning 3.569 Mbp, and the interval for Chromosome 6 QTL is 11 cM covering 1.299 Mbp. The mapped QTLs provide a foundation for map-based cloning of the genes and establishing an understanding of the associated mechanisms underlying GSB resistance in cucumber.     

Detection of downy and powdery mildew resistance QTL in a ‘Regent’ × ‘RedGlobe’ population

One hundred and eighty six F₁ plants from a ‘Regent’ × ‘RedGlobe’ cross were used to generate a partial linkage map with 139 microsatellite markers spanning all 19 chromosomes. Phenotypic scores for downy mildew, taken over two years, confirmed a major resistance QTL (Rpv3) against downy mildew in the interval VVIN16-cjvh to UDV108 on chromosome 18 of ‘Regent’. This locus explained up to 62 % of the phenotypic variance observed. Additionally a putative minor downy mildew resistance locus was observed on chromosome 1 in one season. A major resistance locus against powdery mildew (Ren3) was also identified on chromosome 15 of ‘Regent’ in the interval UDV116 to VChr15CenGen06. This study established the efficacy of and validated the ‘Regent’-derived downy and powdery mildew major resistance genes/QTL under South African conditions. Closely linked SSR markers for marker-assisted selection and gene pyramiding strategies were identified.     

Differential influence of QTL linked to Fusarium head blight,Fusarium-damaged kernel,deoxynivalenol contents and associated morphological traits in a Frontana-derived wheat population

The genetic background of Fusarium head blight (FHB) resistance in the moderately resistant wheat variety Frontana was investigated in the GK Mini Manó/Frontana DH population (n = 168). The plant material was evaluated across seven epidemic environments for FHB, Fusarium-damaged kernel (FDK) and deoxynivalenol (DON) contents caused by two Fusarium species (F. culmorum and F. graminearum). The effects of phenotypic traits such as plant height and heading date were also considered in the experiments. In the population, 527 polymorph markers (DArT, SSR) within a distance of 1,381 cM distance were mapped. The quantitative trait locus/loci (QTL) on chromosomes 4A and 4B demonstrated a significant linkage only with FHB, while QTL on chromosomes 3A, 4B, 7A and 7B were linked to DON accumulation alone. Regions determining all the investigated Fusarium resistance traits were identified on chromosomes 1B, 2D, 3B, 5A, 5B and 6B. The markers in these regions are of the greatest significance from the aspect of resistance breeding. Our results indicate that the genetic background of resistance against FHB, FDK and DON accumulation can differ, and all these traits should be taken under consideration during resistance tests. Moreover, this is the first report on the mapping of Frontana-derived QTL that influence DON accumulation, which is important since the level of DON contamination determines the actions of the food and feed industries. Selection should therefore also focus on this trait by using molecular markers linked to DON content.     

Detection of QTL for forage yield,lodging resistance and spring vigor traits in alfalfa (Medicago sativa L.)

Alfalfa (Medicago sativa L.) is an internationally significant forage crop. Forage yield, lodging resistance and spring vigor are important agronomic traits conditioned by quantitative genetic and environmental effects. The objective of this study was to identify quantitative trait loci (QTL) and molecular markers associated with increased forage yield, resistance to lodging, and spring vigor. A backcross population composed of 128 progeny was developed by crossing the breeding parents DW000577 (lodging susceptible) and NL002724 (lodging-resistant) and back-crossing an individual F₁ plant to the maternal parent (i.e. DW000577). A linkage map of NL002724 was developed based upon the segregation of 236 AFLP, SRAP, and SSR markers among the backcross progeny. The markers were distributed among 14 linkage groups, covering an estimated recombination distance of 1497.6 centiMorgans (cM). Replicated clones of both parents and backcross progeny were evaluated in the field for estimated forage yield, lodging, and spring vigor in Washington and Wisconsin during 2007 and 2008. Significant QTL were found for all three traits. In particular, two QTL for lodging resistance were identified that explained ≥14 % of trait variation, and were significant in all years and locations. Major QTL explaining over 25 % of trait variation for forage yield were detected in multiple environments at two separate locations on chromosome III. Several QTL for spring vigor were located in the same or similar positions as QTL for forage yield, possibly explaining the significant correlation between these traits. Molecular markers associated with the aforementioned QTL were also identified.     

Development of AFLP-derived SCAR markers associated with resistance to two races of southern root-knot nematode in sweetpotato

The southern root-knot nematode (SRKN) Meloidogyne incognita severely damages yield and quality in sweetpotato production, and host plant resistance is one of the primary options for SRKN control. Segregation of F₁ progeny resistant and susceptible to the SP1 and SP2 races of SRKN suggested that the race-specific resistance of the sweetpotato cultivar ??Hi-Starch?? is mostly controlled by single genes and that the genes for resistance against each race are closely located. Bulked segregant analysis and subsequent analysis of 86 F₁ progeny plants identified nine amplified fragment-length polymorphism markers associated with SRKN resistance and a single linkage map consisting of seven of these markers. Quantitative trait locus (QTL) analysis using the segregating resistance data of the F₁ progeny allowed mapping of both a locus with a large effect on resistance to the SRKN race SP1 and another affecting resistance to SP2 to the region around E33M53_090 that was designated as qRmi(t). Two AFLP markers in the vicinity of qRmi(t), E33M53_090 and E41M32_206, were converted to locus-specific sequence-characterized amplified region markers based on their internal and adjacent DNA sequences. These markers might be useful for marker-assisted selection of SRKN resistance in sweetpotato breeding and as a first step to map-based cloning of the responsible QTL(s).     

Genetic analysis of plant height using two immortalized populations of “CRI12 × J8891” in Gossypium hirsutum L.

Plant height is an important plant architecture trait that determines the canopy structure, photosynthetic capacity and lodging resistance of upland cotton populations. To understand the genetic basis of plant height for marker-assisted breeding, quantitative trait loci (QTL) analysis was conducted based on the genetic map of recombinant inbred lines (RILs) derived from the cross “CRI12 × J8891” (Gossypium hirsutum L.). Three methods, including composite interval mapping, multiple interval mapping and multi-marker joint analysis, were used to detect QTL across multiple environments in the RILs and in the immortalized F₂ population developed through intermating between RILs. A total of 19 QTL with genetic main effects and/or genetic × environment interaction effects were identified on 15 chromosomes or linkage groups, each explaining 5.8–14.3 % of the phenotypic variation. Five digenic epistatic QTL pairs, mainly involving additive × additive and/or dominance × dominance, were detected in different environments. Seven out of eight interacting loci were main-effect QTL, suggesting that these loci act as major genes as well as modifying genes in the expression of plant height. The results demonstrate that additive effects, dominance and epistasis are all important for the genetic constitution of plant height, with additive effects playing a more important role in reducing plant height. QTL showing stability across environments that were repeatedly detected by different methods can be used in marker-assisted breeding.     

Identification and marker‐assisted introgression of QTL conferring resistance to bacterial leaf blight in cowpea (Vigna unguiculata (L.) Walp.)

Bacterial leaf blight (BLB), caused by Xanthomonas axonopodis pv. vignicola (Xav), is widespread in major cowpea [Vigna unguiculata (L.) Walp.] growing regions of the world. Considering the resource poor nature of cowpea farmers, development and introduction of cultivars resistant to the disease is the best option. Identification of DNA markers and marker‐assisted selection will increase precision of breeding for resistance to diseases like bacterial leaf blight. Hence, an attempt was made to detect QTL for resistance to BLB using 194 F_2 : 3 progeny derived from the cross ‘C‐152’ (susceptible parent) × ‘V‐16’ (resistant parent). These progeny were screened for resistance to bacterial blight by the leaf inoculation method. Platykurtic distribution of per cent disease index scores indicated quantitative inheritance of resistance to bacterial leaf blight. A genetic map with 96 markers (79 SSR and 17 CISP) constructed from the 194 F₂ individuals was used to perform QTL analysis. Out of three major QTL identified, one was on LG 8 (qtlblb‐1) and two on LG 11 (qtlblb‐2 and qtlblb‐3). The PCR product generated by the primer VuMt337 encoded for RIN2‐like mRNA that positively regulate RPM1‐ and RPS2‐dependent hypersensitive response. The QTL qtlblb‐1 explained 30.58% phenotypic variation followed by qtlblb‐2 and qtlblb‐3 with 10.77% and 10.63%, respectively. The major QTL region on LG 8 was introgressed from cultivar V‐16 into the bacterial leaf blight susceptible variety C‐152 through marker‐assisted backcrossing (MABC).     

Developing new markers and QTL mapping for greenbug resistance in sorghum [Sorghum bicolor (L.) Moench]

Greenbug is a major damaging insect to sorghum production in the United States. Among various virulent greenbug biotypes, biotype I is the most predominant and severe for sorghum. To combat with the damaging pest, greenbug resistant sources were obtained from screening sorghum germplasm collection. This experiment was conducted to identify the genomic regions contributing resistance to greenbug biotype I in a sorghum accession, PI 607900. An F₂ mapping population consisting of 371 individuals developed from a cross of the resistant line with an elite cultivar, BTx623 (susceptible) were tested and scored for their response to greenbug feeding in the greenhouse. Significant differences in resistance were observed between the two parental lines and among their F₂ progeny in response to greenbug feeding at 7, 10, 14 and 21 days after infestation. A linkage map spanning a total length of 729.5 cM across the genome was constructed with 102 polymorphic SSR markers (69 genomic and 33 EST SSRs). Of those microsatellite markers, 48 were newly developed during this study, which are a useful addition for sorghum genotyping and genome mapping. Single marker analysis revealed 29 markers to be significantly associated with the plant response to greenbug feeding damage. The results from interval mapping, composite interval mapping and multiple interval mapping analyses identified four major QTLs for greenbug resistance on chromosome 9. These QTLs collectively accounted for 34–82 % of the phenotypic variance in greenbug resistance. Minor QTLs located on chromosome 3 explained 1 % of the phenotypic variance in greenbug resistance. The major allele for greenbug resistance was on chromosome 9 close to receptor-like kinase Xa21-binding protein 3. These markers are useful to screen more resistant genotypes. Furthermore, the markers tagged to QTL regions can be used to enhance the sorghum breeding program for greenbug resistance through marker-assisted selection and map-based cloning.     

Characterization of Chinese wheat germplasm for resistance to Fusarium head blight at CIMMYT, Mexico

Fusarium head blight (FHB) poses a challenge for wheat breeders worldwide; there are limited sources of resistance and the genetic basis for resistance is not well understood. In the mid-1980s, a shuttle breeding and germplasm exchange program launched between CIMMYT-Mexico and China, enabled the incorporation of FHB resistance from Chinese bread wheat germplasm into CIMMYT wheat. Most of the Chinese wheat materials conserved in the CIMMYT germplasm bank had not been fully characterized for FHB reaction under Mexican environments, until 2009, when 491 Chinese bread wheat lines were evaluated in a FHB screening nursery in Mexico, and 304 (61.9 %) showed FHB indices below 10 %. Subsequent testing occurred in 2010 for plant height (PH), days to heading (DH), and leaf rust response. In 2012, 140 elite lines with good agronomic types were further evaluated for field FHB reaction and deoxynivalenol (DON) accumulation. Most of the tested lines showed good resistance: 116 (82.9 %) entries displayed FHB indices lower than 10 %, while 89 (63.6 %) had DON contents lower than 1.0 ppm. Significant negative correlations were observed between FHB traits (FHB index, DON content, and Fusarium damaged kernels) and PH, DH, and anther extrusion. A subset of 102 elite entries was selected for haplotyping using markers linked to 10 well known FHB quantitative trait loci (QTL). 57 % of the lines possessed the same 2DL QTL marker alleles as Wuhan 1 or CJ 9306, and 26.5 % had the same 3BS QTL allele as Sumai 3. The remaining known QTL were of low frequency. These materials, especially those with none of the above tested resistance QTL (26.5 %), could be used in breeding programs as new resistance sources possessing novel genes for FHB resistance and DON tolerance.     

Identification of QTLs for resistance to Fusarium wilt and Ascochyta blight in a recombinant inbred population of chickpea (<Emphasis Type="Italic">Cicer arietinum</Emphasis> L.)

Fusarium wilt (FW; caused by Fusarium oxysporum f. sp. ciceris) and Ascochyta blight (AB; caused by Ascochyta rabiei) are two major biotic stresses that cause significant yield losses in chickpea (Cicer arietinum L.). In order to identify the genomic regions responsible for resistance to FW and AB, 188 recombinant inbred lines derived from a cross JG 62 × ICCV 05530 were phenotyped for reaction to FW and AB under both controlled environment and field conditions. Significant variation in response to FW and AB was detected at all the locations. A genetic map comprising of 111 markers including 84 simple sequence repeats and 27 single nucleotide polymorphism (SNP) loci spanning 261.60 cM was constructed. Five quantitative trait loci (QTLs) were detected for resistance to FW with phenotypic variance explained from 6.63 to 31.55%. Of the five QTLs, three QTLs including a major QTL on CaLG02 and a minor QTL each on CaLG04 and CaLG06 were identified for resistance to race 1 of FW. For race 3, a major QTL each on CaLG02 and CaLG04 were identified. In the case of AB, one QTL for seedling resistance (SR) against ‘Hisar race’ and a minor QTL each for SR and adult plant resistance against isolate 8 of race 6 (3968) were identified. The QTLs and linked markers identified in this study can be utilized for enhancing the FW and AB resistance in elite cultivars using marker-assisted backcrossing.     

The detection of QTLs controlling bacterial wilt resistance in tobacco (N. tabacum L.)

The bacterial tobacco wilt caused by Ralstonia solanacearum is one of the most destructive soil-borne diseases worldwide. One strategy to improve the resistance to bacterial wilt is to make use of plant varieties expressing wilt resistance genes. To characterize the genetics of wilt resistance and to identify relevant molecular markers for use in plant breeding, quantitative trait loci (QTLs) affecting tobacco bacterial wilt resistance were mapped in the F_2:3 and F_2:4 progeny produced from two crosses between the wilt-resistant breeding lines Enshu and Yanyan97 and the susceptible cultivar TI448A. A linkage map containing 118 loci in 24 linkage groups was constructed for 236 lines from the Enshu×TI448A cross, and a linkage map containing 96 loci in 24 linkage groups was constructed for 264 lines from the Yanyan97×TI448A cross. The wilt resistance of the progeny was examined in field trials conducted in Xuancheng, China, in 2010, 2011, and 2012. The disease severity was assessed on stems using separate rating scales. Mapmaker/EXP 3.0 and Mapmaker/QTL 1.1 were used to identify the qBWR-3a, qBWR-3b, qBWR-5a and qBWR-5b QTLs in linkage group 3 and 5; these four loci were strongly associated with resistance and explain 9.00, 19.70, 17.30, and 17.40 % of the variance in resistance, respectively. The close linkage of the markers PT20275 and PT30229 was detected in both the TI448A×Enshu and TI448A×Yanyan97 crosses, and this linkage group could be used to select individual resistant plants. These findings suggest that one strategy to combat bacterial wilt could be to exploit the resistance genes of the Enshu and Yanyan97 strains.     

Mapping association of molecular markers and sheath blight (<Emphasis Type="Italic">Rhizoctonia solani</Emphasis>) disease resistance and identification of novel resistance sources and loci in rice

Sheath blight (ShB) disease caused by Rhizoctonia solani is one of the major threats to rice crop world-wide. Progress in breeding for resistant rice varieties is limited due to lack of highly resistant germplasm against sheath blight. In present study, diverse rice landrace were phenotyped against R. solani and resistant and moderately resistant sources were identified from the panel of 134 germplasm pool. Landrace Nizam shait showed resistance, where as Bidar local-2, Jigguvaratiga, NavaliSali, Jaddu and Tetep exhibited moderate resistance. Population structure was analysed by genotyping the accessions using 63 genome wide Rice Microsatellite markers which divided the mapping panel into two groups. Association mapping using GLM?+?Q model of TASSEL indicated significant association between twenty-one marker loci on nine chromosomes with ShB resistance with phenotypic variation (R²) ranging 3.02–22.71 per cent. We identified 13 new markers to be associated with ShB resistance. The present work validates previously identified eight markers flanking different shB QTLs. None of the allele from the tested markers was unique and common among resistant and moderately resistant landraces identified in this work except allele 420 bp of RM337 and allele 310 bp of RM5556 noticed only in Tetep. Our findings predict the possible presence of unreported QTL region in marker interval of RM337 and RM5556 on chromosome 8 for ShB resistance in Tetep which invites further investigation.     

Identification and validation of a yield-enhancing QTL cluster in rice (Oryza sativa L.)

Improvement of rice grain yield (YD) is an important goal in rice breeding. YD is determined by its related traits such as spikelet fertility (SF), 1,000-grain weight (TGW), and the number of spikelets per panicle (SPP). We previously mapped quantitative trait loci (QTLs) for SPP and TGW using the recombinant inbred lines (RILs) derived from the crosses between Minghui 63 and Teqing. In this study, four QTLs for SF and four QTLs for YD were detected in the RILs. Comparison of the locations of QTLs for these three yield-related traits identified one QTL cluster in the interval between RM3400 and RM3646 on chromosome 3. The QTL cluster contained three QTLs, SPP3a, SF3 and TGW3a, but no YD QTL was located there. To validate the QTL cluster, a BC₄F₂ population was obtained, in which SPP3a, SF3 and TGW3a were simultaneously mapped to the same region. SPP3a, SF3 and TGW3a explained 36.3, 29.5 and 59.0 % of phenotype variance with additive effect of 16.4 spikelets, 6 % SF and 1.8 g grain weight, respectively. In the BC₄F₂ population, though the region has opposite effects on TGW and SPP/SF, a YD QTL YD3 identified in this cluster region can increase 4.6 g grains per plant, which suggests this QTL cluster is a yield-enhancing QTL cluster and can be targeted to improve rice yield by marker aided selection.     

Common bean breeding for resistance against biotic and abiotic stresses: From classical to MAS breeding

Summary Breeding for resistance to biotic and abiotic stresses of global importance in common bean is reviewed with emphasis on development and application of marker-assisted selection (MAS). The implementation and adoption of MAS in breeding for disease resistance is advanced compared to the implementation of MAS for insect and abiotic stress resistance. Highlighted examples of breeding in common bean using molecular markers reveal the role and success of MAS in gene pyramiding, rapidly deploying resistance genes via marker-assisted backcrossing, enabling simpler detection and selection of resistance genes in absence of the pathogen, and contributing to simplified breeding of complex traits by detection and indirect selection of quantitative trait loci (QTL) with major effects. The current status of MAS in breeding for resistance to angular leaf spot, anthracnose, Bean common mosaic and Bean common mosaic necrosis viruses, Beet curly top virus, Bean golden yellow mosaic virus, common bacterial blight, halo bacterial blight, rust, root rots, and white mold is reviewed in detail. Cumulative mapping of disease resistance traits has revealed new resistance gene clusters while adding to others, and reinforces the co-location of QTL conditioning resistance with specific resistance genes and defense-related genes. Breeding for resistance to insect pests is updated for bean pod weevil (Apion), bruchid seed weevils, leafhopper, thrips, bean fly, and whitefly, including the use of arcelin proteins as selectable markers for resistance to bruchid seed weevils. Breeding for resistance to abiotic stresses concentrates on drought, low soil phosphorus, and improved symbiotic nitrogen fixation. The combination of root growth and morphology traits, phosphorus uptake mechanisms, root acid exudation, and other traits in alleviating phosphorus deficiency, and identification of numerous QTL of relatively minor effect associated with each trait, reveals the complexity to be addressed in breeding for abiotic stress resistance in common bean.