Genomic prediction and GWAS of Gibberella ear rot resistance traits in dent and flint lines of a public maize breeding program

Gibberella ear rot (GER) is a serious threat to maize cultivation, causing grain yield losses and contamination with mycotoxins. Genomic prediction (GP) has great potential to accelerate resistance breeding against GER. However, small training sets (TS) consisting of both phenotyped and genotyped individuals are a challenge for obtaining high prediction accuracy (ρ) in GP. A potential solution would be combining small-size populations across heterotic pools. However, genetic heterogeneity between populations in terms of segregating QTL, linkage disequilibrium (LD) pattern and genomic relationships can impair ρ of GP. In this study, we investigated the genetic architecture of GER severity, deoxynivalenol concentration (DON) and days to silking with genome-wide association studies within two elite panels of 130 dent and 114 flint lines from the maize breeding program of the University of Hohenheim tested in four environments. We also assessed the consistency of LD pattern and genomic relationships between the two heterotic pools. Furthermore, we compared four GP approaches differing in the composition of the TS with lines from a single or combined pool(s) and statistical models with marker effects identical or different but correlated between pools. We detected two and six QTL for DON within the dent and flint pool, respectively, but no common QTL. The LD pattern was consistent between pools for marker pairs ≤ 10 kb apart. GP across pools yielded low or even negative ρ. Combined-pool GP had no higher ρ than within-pool GP, regardless of the statistical model. Our findings underline the importance of investigating the genetic heterogeneity between populations prior to implementing GP using combined TS.     

Genotyping by sequencing of rice interspecific backcross inbred lines identifies QTLs for grain weight and grain length

Grain weight and grain length are the most stable components of rice yield and important indicators of consumer preference. Considering the potentials of wild rice and to enhance the rice yields to meet the increasing demands, 185 Backcross Inbred Lines (BILs) in the background of O. sativa ssp. indica cv. PR114, including 63 rufi-BILs derived from O. rufipogon IRGC104433 and 122 glumae-BILs from O. glumaepatula IRGC104387 were evaluated for mapping QTLs for yield and yield component traits using Genotyping by Sequencing (GBS). Phenotypic evaluation of BILs in three seasons spanning two locations revealed significant differences compared with recurrent parent. BILs which did not show significant differences for any trait under investigation, or similar based on pedigree, were excluded from GBS. Some glumae-BILs had to be excluded from mapping QTLs due to less sequence information. A custom designed approach for GBS data analysis identified 3322 informative SNPs in 55 rufi-BILs and 3437 informative SNPs in 79 glumae-BILs. QTL mapping identified one QTL for thousand grain weight (qtgw5.1), two for grain width (qgw5.1, qgw5.2) and one for grain length (qgl7.1) in rufi-BILs. In the glumae-BILs, three QTL for thousand grain weight (qtgw2.1, qtgw3.1, qtgw6.1) and two for grain length (qgl3.1, qgl7.1) were identified. Most of the grain weight and width QTL showed positive additive effect contributed by wild species allele, whereas the grain length QTL showed positive additive effect contributed by recurrent parent allele. Based on their physical position, none of the QTLs were found similar to previously cloned QTLs. QTLs for grain traits identified from low yielding wild relatives of rice reveals their significance in improving further the rice yields and widen the genetic base of cultivated rice.     

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.     

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.     

Conferring resistance to pre-harvest sprouting in durum wheat by a QTL identified in <Emphasis Type="Italic">Triticum spelta</Emphasis>

Pre-harvest sprouting (PHS) causes significant yield loss and degrade the end-use quality of wheat, especially in regions with prolonged wet weather during the harvesting season. Unfortunately, the gene pool of Triticum durum (tetraploid durum wheat) has narrow genetic base for PHS resistance. Therefore, finding out new genetic resources from other wheat species to develop PHS resistance in durum wheat is of importance. A major PHS resistance QTL, Qphs.sicau-3B.1, was mapped on chromosome 3BL in a recombinant inbred line population derived from ‘CSCR6’ (Triticum spelta), a PHS resistant hexaploid wheat and ‘Lang’, a PHS susceptible Australian hexaploid wheat cultivar. This QTL, Qphs.sicau-3B.1, is positioned between DArT marker wPt-3107 and wPt-6785. Two SCAR markers (Ph3B.1 and Ph3B.2) were developed to track this major QTL and were used to assay a BC₂F₈ tetraploid population derived from a cross between the durum wheat ‘Bellaroi’ (PHS susceptible) and ‘CSCR6’ (PHS resistant). Phenotypic assay and marker-assisted selection revealed five stable tetraploid lines were highly PHS resistant. This study has successfully established that PHS-resistance QTL from hexaploid wheat could be efficiently introgressed into tetraploid durum wheat. This tetraploid wheat germplasm could be useful in developing PHS resistant durum cultivars with higher yield and good end-use quality.     

Identification and characteristics of quantitative trait locus for grain protein content, <Emphasis Type="Italic">TGP12</Emphasis>, in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Grain protein content is an important analysis target to determine grain quality in rice. This study analyzed quantitative trait loci (QTLs) for the content of grain protein and amylose using the chromosomal segment substitution lines developed from ‘Koshihikari’ and ‘Nona Bokra’. It also evaluated the effects of target QTL on eating and cooking quality through the physical properties of cooked rice and its gel consistency. QTL analysis over 3 years detected the QTL on chromosome 12, TGP12, which consistently decreased total grain protein content via the ‘Nona Bokra’ allele. Selected CSSL with TGP12, CSSL-TGP12, showed a lower content of total grain protein in brown and milled rice, and had similar amylose content, grain size, and weight of brown rice, compared with ‘Koshihikari’. Based on the results of sodium dodecyl sulfate polyacrylamide gel electrophoresis, brown rice with CSSL-TGP12 had no remarkable decrease or loss in any specific protein. Regarding eating and cooking quality, CSSL-TGP12 did not show stable effects on physical properties, hardness, stickiness, or adherability of cooked rice or its gel consistency. These results suggest that TGP12 could be one of the key genetic factors for the alteration of grain protein content without an effect on eating or cooking quality.     

Genetic dissection of rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) tiller,plant height,and grain yield based on QTL mapping and metaanalysis

Tiller number per plant (TN) and plant height (PH) are important agronomic traits related to grain yield (GY) in rice (Oryza sativa L.). A total of 30 additive quantitative trait loci (A-QTL) and 9 significant additive × environment interaction QTLs (AE-QTL) were detected, while the phenotypic and QTL correlations confirmed the intrinsic relationship of the three traits. These QTLs were integrated with 986 QTLs from previous studies by metaanalysis. Consensus maps contained 7156 markers for a total map length of 1112.71 cM, onto which 863 QTLs were projected; 78 meta-QTLs (MQTLs) covering 11 of the 30 QTLs were detected from the cross between Dongnong422 and Kongyu131 in this study. A total of 705 predicted genes were distributed over the 21 MQTL intervals with physical length <0.3 Mb; 13 of the 21 MQTLs, and 34 candidate genes related to grain yield and plant development, were screened. Five major QTLs, viz. qGY6-2, qPH7-2, qPH6-3, qTN6-1, and qTN7-1, were not detected in the MQTL intervals and could be used as newly discovered QTLs. Candidate genes within these QTL intervals will play a meaningful role in molecular marker-assisted selection and map-based cloning of rice TN, PH, and GY.     

QTL mapping and analysis of epistatic interactions for grain yield and yield-related traits in <Emphasis Type="Italic">Triticum turgidum</Emphasis> L. var. <Emphasis Type="Italic">durum</Emphasis>

A quantitative trait loci (QTL) analysis of grain yield and yield-related traits was performed on 93 durum wheat recombinant inbred lines derived from the cross UC1113 × Kofa. The mapping population and parental lines were analyzed considering 19 traits assessed in different Argentine environments, namely grain yield, heading date, flowering time, plant height, biomass per plant, and spikelet number per ear, among others. A total of 224 QTL with logarithm of odds ratio (LOD) ≥ 3 and 47 additional QTL with LOD > 2.0 were detected. These QTL were clustered in 35 regions with overlapping QTL, and 12 genomic regions were associated with only one phenotypic trait. The regions with the highest number of multi-trait and stable QTL were 3BS.1, 3BS.2, 2BS.1, 1BL.1, 3AL.1, 1AS, and 4AL.3. The effects of epistatic QTL and QTL × environment interactions were also analyzed. QTL putatively located at major gene loci (Rht, Vrn, Eps, and Ppd) as well as additional major/minor QTL involved in the complex genetic basis of yield-related traits expressed in Argentine environments were identified. Interestingly, the 3AL.1 region was found to increase yield without altering grain quality or crop phenology.     

Analysis of QTL for seed oil content in <Emphasis Type="Italic">Brassica napus</Emphasis> by association mapping and QTL mapping

Increasing seed oil content is one of the most important breeding targets for rapeseed (Brassica napus). In this study, we combined quantitative trait loci (QTL) mapping and marker-trait association analysis to dissect the genetic basis of seed oil content in rapeseed. A doubled haploid (DH) population with 261 lines was grown in two highly contrasting macro-environments, Germany with winter ecotype environment and China with semi-winter ecotype environment, to explore the effect of environment effect of on seed oil content. Notable macro-environment effect was found for seed oil content. 19 QTL for seed oil content were identified across the two macro-environments. For association analysis, a total of 142 rapeseed breeding lines with diverse oil contents were grow in China macro-environment. We identified 23 simple sequence repeat (SSR) markers that were significantly associated with the seed oil content. Comparative analysis revealed that five QTL identified in the DH population, located on chromosomes A03, A09, A10 and C09, were co-localized with 11 significantly associated SSR markers that were identified from the association mapping population. Of which, the QTL on chromosome A10 was found to be homeologous with the QTL on chromosome C09 by aligning QTL confidence intervals with the reference genomes B. napus. Those QTL associated with specific macro-environments provides valuable insight into the genetic regulation of seed oil content and will facilitate marker-assisted breeding of B. napus.     

Rapid identification of a major effect QTL conferring adult plant resistance to stripe rust in wheat cultivar Yaco“S”

Stripe rust is a devastating disease in common wheat (Triticum aestivum) worldwide. Growing cultivars with adult-plant resistance (APR) is an environmental friendly approach that provides long-term protection to wheat from this disease. Wheat cultivar Yaco“S” showed a high level of APR to stripe rust in the field from 2008 to 2014. The objective of this study was to detect the major quantitative trait loci (QTL) for APR to stripe rust in Yaco“S”. One hundred and eighty-four F_2:3 lines were developed from a cross between Yaco“S” and susceptible cultivar Mingxian169. Illumina 90K and 660K single nucleotide polymorphism (SNP) chips were implemented to bulked pools and their parents to identify SNPs associated with the major QTL. A high-density linkage map was constructed using simple sequence repeat (SSR) and SNP markers. Inclusive composite interval mapping detected a major effect QTL Qyryac.nwafu-2BS conferring stable resistance to stripe rust in all tested environments. Qyryac.nwafu-2BS were mapped to a 1.3 cm interval and explained 17.3–51.9% of the phenotypic variation. Compared with stripe rust resistance genes previously mapped to chromosome 2B, Qyryac.nwafu-2BS is likely a new APR gene to stripe rust. Combining SNP iSelect assay and kompetitive allele specific PCR technology, we found that the APR gene could be rapidly and accurately mapped and it is useful for improving stripe rust resistance in wheat breeding.     

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.     

QTL for flag leaf size and their influence on yield-related traits in wheat

Flag leaf-related traits (FLRTs) are determinant traits affecting plant architecture and yield potential in wheat (Triticum aestivum L.). In this study, three related recombinant inbred line (RIL) populations with a common female parent were developed to identify quantitative trait loci (QTL) for flag leaf width (FLW), length (FLL), and area (FLA) in four environments. A total of 31 QTL were detected in four environments. Two QTL for FLL on chromosomes 3B and 4A (QFll-3B and QFll-4A) and one for FLW on chromosome 2A (QFlw-2A) were major stable QTL. Ten QTL clusters (C1–C10) simultaneously controlling FLRTs and yield-related traits (YRTs) were identified. To investigate the genetic relationship between FLRTs and YRTs, correlation analysis was conducted. FLRTs were found to be positively correlated with YRTs especially with kernel weight per spike and kernel number per spike in all the three RIL populations and negatively correlated with spike number per plant. Appropriate flag leaf size could benefit the formation of high yield potential. This study laid a genetic foundation for improving yield potential in wheat molecular breeding programs.     

Identification of novel quantitative trait loci associated with brown planthopper resistance in the rice landrace Salkathi

The brown planthopper (BPH) is a potent pest of rice in Asia and Southeast Asia. Host resistance has been found to be the most suitable alternative to manage the insect. But varietal resistance has been found to be short-lived. There has been a constant search for alternate resistance genes. We developed an F₈ recombinant inbred population for the BPH resistance gene in Salkathi, an indica landrace from Odisha, India. Phenotyping of RILs against the BPH population at Cuttack, Odisha showed continuous skewed variation with four peaks at 2.1–3.0, 4.1–5.0, 6.1–7.0 and 8.1–9.0 SES score, suggesting the involvement of quantitative loci for resistance to BPH in Salkathi. Mapping showed the presence of two QTLs on the short arm of chromosome 4. One QTL, with phenotype variance of 37.02% is located between the markers RM551 and RM335. The other QTL, with phenotype variance of 7.1% is located between markers RM335 and RM5633. The two QTLs have been designated as qBph4.3 and qBph4.4. QBph4.3 seems to be a novel QTL associated with BPH resistance. We have successfully transferred qBph4.3 and qBph4.4 into two elite rice cultivars, Pusa 44 and Samba Mahsuri. Fine mapping of the identified QTLs may lead to a successful transfer of QTLs into other elite germplasm backgrounds.     

Analysis of population structure and genetic diversity reveals gene flow and geographic patterns in cultivated rice (<Emphasis Type="Italic">O. sativa</Emphasis> and <Emphasis Type="Italic">O. glaberrima</Emphasis>) in West Africa

To fully exploit the diversity in African rice germplasm and to broaden the gene pool reliable information on the population genetic diversity and phenotypic characteristics is a prerequisite. In this paper, the population structure and genetic diversity of 42 cultivated African rice (Oryza spp.) accessions originating from West Africa (Benin, Mali and Nigeria, Liberia etc.) were investigated using 20 simple sequence repeats (SSR) and 77 amplified fragment length polymorphisms (AFLP). Additionally, field trials were set up to gain insight into phenotypic characteristics that differentiate the genetic populations among rice accessions. The analysis revealed considerably high polymorphisms for SSR markers (PIC mean?=?0.78) in the germplasm studied. A significant association was found between AFLP markers and geographic origin of rice accessions (R?=?0.72). Germplasm structure showed that Oryza sativa accessions were not totally isolated from Oryza glaberrima accessions. The results allowed identification of five O. glaberrima accessions which grouped together with O. sativa accessions, sharing common alleles of 18 loci out of the 20 SSR markers analyzed. Population structure analysis revealed existence of a gene flow between O. sativa and O. glaberrima rice accessions which can be used to combine several interesting traits in breeding programs. Further studies are needed to clarify the contributions of this gene flow to valuable traits such as abiotic and biotic stresses including disease resistance.     

Genetic mapping of resistance to <Emphasis Type="Italic">Puccinia hordei</Emphasis> in three barley doubled-haploid populations

The success of breeding for barley leaf rust (BLR) resistance relies on regular discovery, characterization and mapping of new resistance sources. Greenhouse and field studies revealed that the barley cultivars Baronesse, Patty and RAH1995 carry good levels of adult plant resistance (APR) to BLR. Doubled haploid populations [(Baronesse/Stirling (B/S), Patty/Tallon (P/T) and RAH1995/Baudin (R/B)] were investigated in this study to understand inheritance and map resistance to BLR. The seedlings of two populations (B/S and R/B) segregated for leaf rust response that conformed to a single gene ratio (\({\text{X}}_{1:1}^{2}\) = 0.12, P > 0.7 for B/S and \({\text{X}}_{1:1}^{2}\) = 0.34, P > 0.5 for R/B) whereas seedlings of third population (P/T) segregated for two-gene ratio (\({\text{X}}_{1:1}^{2}\) = 0.17, P > 0.6) when tested in greenhouse. It was concluded that the single gene in Baudin and one of the two genes in Tallon is likely Rph12, whereas gene responsible for seedling resistance in Stirling is Rph9.am (allele of Rph12). The second seedling gene in Tallon is uncharacterized. In the field, APR was noted in lines that were susceptible as seedlings. A range of disease responses (CI 5–90) was observed in all three populations. Marker trait association analysis detected three QTLs each in populations B/S (QRph.sun-2H.1, QRph.sun-5H.1 and QRph.sun-6H.1) and R/B (QRph.sun-1H, QRph.sun-2H.2, QRph.sun-3H and QRph.sun-6H.2), and four QTLs in population P/T (QRph.sun-6H.2, QRph.sun-1H.2, QRph.sun-5H.2 and QRph.sun-7H) that significantly contributed to low leaf rust disease coefficients. High frequency of QRph. sun-5H.1, QRph. sun-6H.1, QRph. sun-1H.1, QRph. sun-2H.2, QRph. sun-6H.2, QRph. sun-7H (based on presence of the marker, closely associated to the respective QTLs) was observed in international commercial barley germplasm and hence providing an opportunity for rapid integration into breeding programmes. The identified candidate markers closely linked to these QTLs will assist in selecting and assembling new APR gene combinations; expectantly this will help in achieving good levels of durable resistance for controlling BLR.     

Broad spectrum insect resistance and metabolites in close relatives of the cultivated tomato

Wild relatives of tomato possess effective means to deal with several pests, among which are a variety of insects. Here we studied the presence of resistance components against Trialeurodes vaporariorum, Myzus persicae, Frankliniella occidentalis, and Spodoptera exigua in the Lycopersicon group of Solanum section Lycopersicon by means of bioassays and comprehensive metabolite profiling. Broad spectrum resistance was found in Solanum galapagense and a few accessions of S. pimpinellifolium. Resistance to the sap sucking insects may be based on the same mechanism, but different from the caterpillar resistance. Large and highly significant differences in the leaf metabolomes were found between S. galapagense, containing type IV trichomes, and its closest relative S. cheesmaniae, which lacks type IV trichomes. The most evident differences were the relatively high levels of different methylated forms of the flavonoid myricetin and many acyl sucrose structures in S. galapagense. Possible candidate genes regulating the production of these compounds were identified in the Wf-1 QTL region of S. galapagense, which was previously shown to confer resistance to the whitefly B. tabaci. The broad spectrum insect resistance identified in S. galapagense will be very useful to increase resistance in cultivated tomato.     

Phenotypic and genotypic screening for rust resistance in common bean germplasm in Uganda

Rust caused by Uromyces appendiculatus (Pers., Pers.) Unger is one of the major foliar diseases of common bean (Phaseolus vulgaris) in Uganda. The use of host resistance remains the best option in managing this disease. The objective of this study was to identify sources of broad-spectrum rust resistance in common bean germplasm including landraces, commercial cultivars and introduced genotypes using a combination of phenotypic and genotypic screening with 22 simple sequence repeat (SSR) markers located on chromosome Pv04. A total of 138 genotypes were field screened from 2014 and 2015 using an alpha lattice design. The variance and correlation of disease incidence, area under the disease progression curve (AUDPC) and total grain yield were computed using GenStat. The polymorphism information content of the genotypes was determined, and the association of the markers and the disease resistance traits were analyzed using PowerMarker and TASSEL respectively. Resistance of each genotype was compared to the presence and absence of amplified markers. There were highly significant differences (P < 0.001) among the genotypes for disease incidence, AUDPC and total grain yield and a strong correlation (P < 0.001) between disease incidence and AUDPC in both years. The SSR markers, BARC_PV_SSR04725, bean_ssr_0778 and bean_ssr_2892 were associated (P ≤ 0.05) with rust resistance. Fifteen 15 genotypes which included the landraces Nabufumbo, and Kapchorwa white, and the commercial cultivar NABE 2 were identified as new sources of rust resistance that would be useful in future bean breeding programmes in Uganda.     

Effects of introgressions from <Emphasis Type="Italic">Festuca pratensis</Emphasis> on winter hardiness of <Emphasis Type="Italic">Lolium perenne</Emphasis>

Previous studies reported that some genotypes with introgressed Festuca chromosome segment(s) in Lolium genome showed enhanced winter hardiness compared to Lolium. The aim of this study was to search comprehensively for the Festuca pratensis chromosome regions affecting winter hardiness-related traits when introgressed into the Lolium perenne genome. Association between F. pratensis introgression and winter hardiness-related traits (fall and winter hardiness indexes, early-spring dry matter yield, and freezing tolerance) were screened in the diploid introgression populations (n = 203) that had some F. pratensis chromosome segments introgressed. Eighty-four intron markers corresponding to unique rice genes randomly distributed across the genome were used for genotyping. Winter hardiness of almost all plants in the introgression populations was lower than that of the F. pratensis and triploid hybrid parents, but the average was higher than that of L. perenne. A significant positive effect of F. pratensis introgression on early-spring dry matter yield was detected on chromosome 7. This quantitative trait locus (QTL) was confirmed by linkage analysis using a backcross population with F. pratensis introgression in the target region of chromosome 7. However, the contribution of the newly identified QTL was rather small (6.7–9.6%), suggesting that superior winter hardiness of F. pratensis compared to L. perenne is conferred by multiple small-effect QTLs. We also detected a previously unreported negative effect of Festuca introgression on winter hardiness. Newly obtained QTL information in this study would contribute to the design of Festuca/Lolium hybrid breeding.     

Mapping quantitative trait loci for tolerance to phosphorus-deficiency at the seedling stage in barley

Phosphorus (P) deficiency in soil is a major factor that limits barley yield production. Increasing the tolerance to P-deficiency of barley is one of the most cost-effective solutions. Quantitative trait loci (QTLs) controlling P acquisition, P utilization efficiency and biomass at the seedling stage were identified using a population of recombinant inbred lines (RILs) subjected to two P concentrations (low P (LP), 25 µM and normal P (NP), 250 µM). The population was derived from a cross between Baudin and CN4027, which is a Hordeum spontaneum accession. In two hydroponic trials conducted in 2014 and 2016, seventeen QTLs were detected on chromosomes 2H, 3H, 4H and 5H at the two P concentrations. Eight of these QTLs influenced P acquisition efficiency (PAE). Phenotypic variation explained by a particular PAE-related QTL ranged from 13.3 to 39.9%. One QTL designated as Qspue.sau-3H.01 was related to P utilization efficiency (PUE); the phenotypic variation explained by this QTL was 12.5% (NP concentration) and 13.1% (LP concentration), respectively. Strong associations were observed between biomass and P efficiency-related traits in our study. Two QTL clusters controlling biomass, PAE- and PUE-related traits simultaneously were stably identified in the intervals bPb3263664–bPb3931069 and bPb3264570–bPb4786261 on chromosome 3H at both P concentrations in both trials. The QTLs related to PAE, PUE and biomass are important for the P-tolerant phenotype and may offer valuable clues for fine mapping and map-based cloning of barley.     

Complementary DNA (cDNA) cloning and functional verification of resistance to head smut disease (<Emphasis Type="Italic">Sphacelotheca reiliana</Emphasis>) of an NBS–LRR gene <Emphasis Type="Italic">ZmNL</Emphasis> in maize (<Emphasis Type="Italic">Zea mays</Emphasis>)

The nucleotide-binding site (NBS)-leucine-rich repeat (LRR) gene family comprises the largest number of known disease resistance (R) genes and is one of the largest gene families in plants. In the present study, the full-length cDNA of ZmNL (GenBank Accession Number KF765443) was isolated using Rapid Amplification of cDNA Ends. The nucleotide sequence of ZmNL contains an open reading frame of 3156 bp that encodes the ZmNL protein, which is comprised of 1051 amino acid residues. This putative protein has high homology to other known resistance proteins (84% to Triticum aestivum LR10) and belongs to the CC–NBS–LRR type R gene family. The ZmNL gene was introduced into the maize inbred line of Huangzao4 which was highly susceptible to head smut under the control of the maize ubiquitin promoter by Agrobacterium-mediated transformation. The head smut disease incidence of 3 T₂ transgenic lines was significantly reduced (by 18.38–29.40%) compared with the wild type, which indicated that the overexpression of ZmNL gene in maize enhanced the resistance to the fungus Sporisorium reilianum (Kühn) Clint of these plants.