Mapping quantitative trait loci and expressed sequence tags related to brown planthopper resistance in rice

To map genes responsible for brown planthopper (BPH) resistance in rice, a rice genetic map was constructed based on a recombinant inbred line population from a cross between a BPH‐resistant line ‘B5’ and a susceptible variety ‘Minghui 63’. Four quantitative trait loci (QTLs) for BPH resistance were detected. ESTs differentially regulated by BPH feeding were isolated by suppressive subtractive hybridization (SSH) and assigned to chromosomes based on RFLP mapping and searches of the rice genome database. The distribution of ESTs showed some clustering, and some ESTs are related to known QTLs and known BPH resistance genes. These findings suggest that the mapping of differentially induced ESTs may be a useful strategy for the identification of candidate plant defence genes, which could be beneficial in the development of a BPH‐resistant rice variety.     

Detection of quantitative trait loci (QTL) associated with resistance to whitebacked planthopper (Sogatella furcifera) in rice (Oryza sativa)

Whitebacked planthopper (WBPH) is an important insect pest of rice. In this study, we report quantitative trait loci (QTL) associated with resistance to WBPH using a doubled‐haploid (DH) mapping population derived from the cross IR64/Azucena. We evaluated a set of 91 DH lines using various screening tests which measure seedling resistance, antibiosis and tolerance to WBPH. QTL analysis involving a RFLP map of 175 markers detected a significant QTL on chromosome 7 (RG511‐RG477) associated with seedling resistance to WBPH. In addition, QTL analysis involving available defence related candidate genes as markers on a sub set of 60 DH lines showed significant association of genomic regions on chromosome 1 (W1‐pMRF1), 2 (XLRfrI7‐RG157) and 7 (RG711‐CDO418) with resistance to WBPH. Several suggestive QTL were detected on chromosomes 2, 3, 6, 7, 8 and 11 showing the possibility of their association with resistance to WBPH. The phenotypic contribution of the QTL ranged from 8.4% to 32.1%. Some of the WBPH resistance QTL detected in this study showed similar map positions with the QTL reported for resistance to brown planthopper (BPH) in the same mapping population. These results would be useful for attempts to trace the genes associated with resistance to planthoppers in rice.     

Identification of quantitative trait loci for Cd and Zn concentrations of brown rice grown in Cd-polluted soils

Low grain cadmium (Cd) and high grain zinc (Zn) rice cultivars have become the current rice breeding objectives. However, the genetic control of Cd and Zn concentrations in brown rice remains poorly understood, especially when grown in Cd-contaminated soil. In this study, quantitative trait loci (QTLs) associated with grain Cd and Zn concentrations and Cd/Zn ratio were identified using a doubled haploid population derived from a cross between japonica JX17 and indica ZYQ8 rice cultivars. Three and two QTLs were detected for Cd and Zn concentration in brown rice, respectively. Two QTLs associated with grain Cd/Zn ratio on chromosomes 3 and 6 were initially mapped. These QTLs accounted for 10.83–41.66% of the total variance of the three traits measured. Only one common locus on chromosome 6 was found for Cd concentration and Cd/Zn ratio. The lack of co-location of the QTLs for Cd and Zn concentrations in this mapping population suggests different genetic mechanisms. In summary, our results provide insight into the genetic basis of rice grain Cd and Zn accumulation; the isolated QTLs may be useful for marker-assisted selection and identification of genes associated with Cd and Zn accumulation in rice.     

Identification of quantitative trait loci associated with boiled seed hardness in soybean

Boiled seed hardness is an important factor in the processing of soybean food products such as nimame and natto. Little information is available on the genetic basis for boiled seed hardness, despite the wide variation in this trait. DNA markers linked to the gene controlling this trait should be useful in soybean breeding programs because of the difficulty of its evaluation. In this report, quantitative trait locus (QTL) analysis was performed to reveal the genetic factors associated with boiled seed hardness using a recombinant inbred line population developed from a cross between two Japanese cultivars, ‘Natto-shoryu’ and ‘Hyoukei-kuro 3’, which differ largely in boiled seed hardness, which in ‘Natto-shoryu’ is about twice that of ‘Hyoukei-kuro 3’. Two significantly stable QTLs, qHbs3-1 and qHbs6-1, were identified on chromosomes 3 and 6, for which the ‘Hyoukei-kuro 3’ alleles contribute to decrease boiled seed hardness for both QTLs. qHbs3-1 also showed significant effects in progeny of a residual heterozygous line and in a different segregating population. Given its substantial effect on boiled seed hardness, SSR markers closely linked to qHbs3-1, such as BARCSOYSSR_03_0165 and BARCSOYSSR_03_0185, could be useful for marker-assisted selection in soybean breeding.     

Identification of quantitative trait loci associated with iron deficiency chlorosis resistance in groundnut (Arachis hypogaea)

Iron deficiency chlorosis is an important abiotic stress affecting groundnut production worldwide in calcareous and alkaline soils with a pH of 7.5–8.5. To identify genomic regions controlling iron deficiency chlorosis resistance in groundnut, the recombinant inbred line population from the cross TAG 24 × ICGV 86031 was evaluated for associated traits like visual chlorosis rating and SPAD chlorophyll meter reading across three crop growth stages for two consecutive years. Thirty-two QTLs were identified for visual chlorosis rating (3.9%–31.8% phenotypic variance explained [PVE]) and SPAD chlorophyll meter reading [3.8%–11% PVE] across three stages over 2 years. This is the first report of identification of QTLs for iron deficiency chlorosis resistance-associated traits in groundnut. Three major QTLs (>10% PVE) were identified at severe stage, while majority of other QTLs were having small effects. Interestingly, two major QTLs for visual chlorosis rating at 60 days (2013) and 90 days (2014) were located at same position on LG AhXIII. The identified QTLs/markers after validation across diverse genetic material could be used in genomics-assisted breeding.     

Identification of quantitative trait loci for resistance to bending-type lodging in rice (Oryza sativa L.)

Bending-type lodging is one of the most important factors affecting the yield and grain quality of rice. This study identified quantitative trait loci (QTLs) for physical strength of the upper culms, and evaluated QTL effects on lodging resistance. In 2010 and 2011, QTLs for breaking strength, length, and diameter of the top three internodes were identified by analyzing chromosomal segment substitution lines (CSSLs) developed from ‘Koshihikari’ and ‘Kasalath’. The QTL analysis indicated that ‘Kasalath’ had two types of QTLs: one to strengthen specific internodes and one to simultaneously improve the physical strengths of plural internodes or the top three internodes. A QTL for breaking strengths of the top three internodes (bsuc11) was detected on chromosome 11 in both years. This QTL did not overlap with that for internode length. To evaluate the effects of bsuc11 on lodging resistance, this study selected three CSSLs with bsuc11 and analyzed the breaking strengths of the top three internodes after heading and the pushing resistance of the lower part. Internodes of ‘Koshihikari’ showed decreased breaking strengths after grain filling, while those of CSSLs with bsuc11 did not show this decrease in breaking strength. The pushing resistance of the lower part at the fully ripe stage was the same in ‘Koshihikari’ and CSSLs with bsuc11. These results suggested that bsuc11 could be a target to improve the physical strength of the upper culms to resist bending-type lodging, and that the physical strengths of upper and lower parts are controlled by different genetic factors in rice.     

Identification and validation of quantitative trait loci associated with seed yield in soybean

In soybean [Glycine max (L.) Merrill], the genetic analysis of seed yield is important to aid in the breeding of high-yielding cultivars. Seed yield is a complex trait, and the number of quantitative trait loci (QTL) involved in seed yield is high. The aims of this study were to identify QTL associated with seed yield and validate their effects on seed yield using near-isogenic lines. The QTL analysis was conducted using a recombinant inbred line population derived from a cross between Japanese cultivars ‘Toyoharuka’ and ‘Toyomusume’, and eight seed yield-associated QTL were identified. There were significant positive correlations between seed yield and the number of favorable alleles at QTL associated with seed yield in the recombinant inbred lines for three years. The effects of qSY8-1, a QTL promoting greater seed yield, was validated in the Toyoharuka background. In a two-year yield trial, the 100-seed weight and seed yield of Toyoharuka-NIL, the near-isogenic line having the Toyomusume allele at qSY8-1, were significantly greater than those of Toyoharuka (106% and 107%, respectively) without any change for days to flowering and maturity. Our results suggest that qSY8-1 was not associated with maturity genes, and contributed to the 100-seed weight.     

Identification and comparative analysis of quantitative trait loci associated with parthenocarpy in processing cucumber

Parthenocarpy (seedless fruit) is an economically important yield‐related trait in cucumber (Cucumis sativus L.; 2n = 2x = 14). However, the genomic locations of factors controlling parthenocarpic fruit development in this species are not known. Therefore, an F_{2 : 3} mating design was utilized to map quantitative trait loci (QTL) for parthenocarpy using a narrow cross employing two gynoecious, indeterminate and normal leaf lines [2A (parthenocarpic) and Gy8 (non‐parthenocarpic)]. QTL detection was performed employing 2A‐ and Gy8‐coupling phase data using the parthenocarpic yield of 126 F₃ families grown at two locations at Hancock, WI in 2000. The QTLs detected in this study were compared with the map locations of QTLs conditioning first‐harvest yield of seeded cucumber characterized in a previous study. There were 10 QTLs for parthenocarpy detected defining four genomic regions, in which three QTLs also mapped to the same genomic regions as QTLs detected for fruit yield at first‐harvest as reported in a previous study. The eight fluorescence amplified fragment length polymorphism (AFLP) markers linked to parthenocarpy through QTL mapping defined herein (four each in linkage groups 1 and 4) are candidates for use in marker‐assisted selection programmes where breeding for increased levels of parthenocarpy is an objective in the elite‐processing cucumber populations.     

Identification of a RAPD marker linked to a brown planthopper resistance gene in rice

We report the tagging of a brown planthopper (BPH) resistance gene (Bph–1) in rice using RAPD and RFLP markers. The Korean rice variety ‘Gayabyeo’ has dominant duplicate genes including Bph–1 conferring resistance to biotype 1 of BPH. Bulked segregant RAPD analysis was employed for rapid identification of DNA markers linked to resistance genes. For tagging these two genes, an F2F3 population from a ‘Gayabyeo’ × ‘Nagdongbyeo’ cross was developed and evaluated for BPH resistance. Three bulked DNAs from two groups of homozygous BPH resistant (each for Bph–1 and the other unknown gene) and homozygous susceptible F2 plants were analyzed by RAPD using 140 random oligomers. One primer, OPD–7 yielded a 700-bp fragment that was present in Gayabyeo and resistant F2 plants (homozygous for Bph-1 locus) but absent in Nagdongbyeo and susceptible F2 plants. Cosegregation of this marker with Bph-1 was verified using an F2 population segregating for Bph-1. Chromosomal regions surrounding the Bph-1 were examined with additional RFLP and microsatellite markers on chromosome 12 to define the location of the RAPD marker and Bph-1. Use of this RAPD marker could facilitate early selection of resistant lines for BPH. This revised version was published online in July 2006 with corrections to the Cover Date.     

Validation of quantitative trait loci for aluminum tolerance in Chinese wheat landrace FSW

Aluminum (Al) toxicity is one of the major constraints for wheat production in acidic soils worldwide and use of Al-tolerant cultivars is one of the most effective approaches to reduce Al damage in the acidic soils. A Chinese landrace, FSW, shows a high level of tolerance to Al toxicity and a mapping population of recombinant inbred lines (RILs) was developed from a cross between FSW and Al-sensitive US spring wheat cultivar Wheaton to validate the quantitative trait loci (QTL) previously identified in FSW. The mapping population was evaluated for net root growth (NRG) during Al stress in a nutrient solution culture and hematoxylin staining score (HSS) of root tips after Al stress. After 132 simple sequence repeat (SSR) markers from three chromosomes that were previously reported to have the QTLs were analyzed in the population, two QTLs for Al tolerance from FSW were confirmed. The major QTL on chromosome 4DL co-segregated with the Al-activated malate transporter gene (ALMT1), however, sequence analysis of the promoter region (Ups4) of ALMT1 gene indicated that FSW contained a marker allele that is different from the one that was reported to condition Al tolerance in the Brazilian source. Another QTL on chromosome 3BL showed a minor effect on Al tolerance in the population. The two QTLs accounted for about 74.9 % of the phenotypic variation for HSS and 72.1 % for NRG and demonstrated an epistatic effect for both HSS and NRG. SSR markers closely linked to the QTLs have potential to be used for marker-assisted selection (MAS) to improve Al tolerance in wheat breeding programs.     

Identification and characterization of quantitative trait loci related to lodging resistance and associated traits in bread wheat

Lodging is a major constraint to increasing yield in many crops, but is of particular importance in the small‐grained cereals. This study investigated the genetic control of lodging and component traits in wheat through the detection of underlying quantitative trait loci (QTL), The analysis was based on the identification of genomic regions which affect various traits related to lodging resistance in a population of 96‐doubled haploid lines of the cross ‘Milan’בCatbird’, mapped using 126‐microsatellite markers. Although major genes related to plant height (Rht genes) were responsible for increasing lodging resistance in this cross, several other traits independent of plant height were shown to be important such as fool and shoot traits, and various components of plant yield. Yield components such as grain number and weight were shown to be an indicator of plant susceptibility to lodging. QTL for lodging and associated traits were found on chromosomes IB, ID. 2B. 2D. 4B, 4D. 6D and 7D. QTL for yield and associated traits were identified on chromosomes IB, ID. 2A. 2B. 2D. 4D and 6A,     

Identification of quantitative trait loci underlying resistance of soybean to Fusarium graminearum

Fusarium graminearum could cause serious yield loss of soybean. Host resistance could offer an economical and effective way to control F. graminearum. The aims of this study were to identify and confirm quantitative trait loci (QTLs) underlying resistance to F. graminearum, and to analyse the genetic effects of pyramid resistance QTL on resistance level. A total of 140 F_2:14 recombinant inbred lines (RILs) were constructed via the cross between 'Hefeng 25' (moderate resistance to F. graminearum) and 'Conrad' (resistance to F. graminearum). The molecular genetic linkage map was constructed based on 164 simple sequence repeat (SSR) markers. A total of seven QTLs underlying F. graminearum resistance, located on six chromosomes, were identified. Among these seven identified QTLs, beneficial allele of qFG-1, qFG-2 and qFG-3 derived from 'Hefeng 25' and beneficial allele of qFG-4, qFG-5, qFG-6, qFG-7 derived from 'Conrad'. Of these seven identified QTLs, qFG-1, qFG-3, qFG-4 and qFG-5 were novel for F. graminearum resistance. Four pairs of QTLs with significant epistatic effects were found. The accumulation of resistance QTL was positively correlated with decreases in disease severity index, which was valuable for improving efficiency of marker-assistant breeding in F. graminearum resistance.     

Genomewide association study reveals novel quantitative trait loci associated with resistance towards Septoria tritici blotch in North European winter wheat

Fungal diseases are a major constraint for wheat production. Effective disease resistance is essential for ensuring a high production quality and yield. One of the most severe fungal diseases of wheat is Septoria tritici blotch (STB), which influences wheat production across the world. In this study, genomewide association mapping was used to identify new chromosomal regions on the wheat genome conferring effective resistance towards STB. A winter wheat population of 164 North European varieties and breeding lines was genotyped with 15K single nucleotide polymorphism (SNP) wheat array. The varieties were evaluated for STB in field trials at three locations in Denmark and across 3 years. The association analysis revealed four quantitative trait loci, on chromosomes 1B, 2A, 5D and 7A, highly associated with STB resistance. By comparing varieties containing several quantitative trait loci (QTL) with varieties containing none of the found QTL, a significant difference was found in the mean disease score. This indicates that an effective resistance can be obtained by pyramiding several QTL.     

Quantitative trait loci for resistance to Fusarium head blight in the Chinese wheat landrace Huangfangzhu

The Chinese wheat landrace Huangfangzhu (HFZ) has a high level of resistance to Fusarium head blight (FHB). To identify chromosomal regions that are responsible for FHB resistance in HFZ, F₈ recombinant inbred lines (RIL) were developed from a cross between HFZ and Wheaton, a U.S. hard spring wheat. FHB was evaluated by single floret inoculation in both greenhouse and field environments. Two quantitative trait loci (QTL) with major effects were identified. One QTL was located on the short arm of chromosome 3B, and explained 35.4% of the phenotypic variation; the other QTL was assigned to 7AL and explained 18.0% of the phenotypic variation for FHB response. In addition, three minor QTL were detected on chromosomes 1AS, 1B and 5AS by single marker regression. HFZ contributed all favorable alleles. The RIL with HFZ alleles at the QTL on 3BS and 7AL displayed significantly lower percentages of infected spikelets than RIL without these alleles in both greenhouse and field environments. HFZ combined several alleles from germplasm reported previously and is a promising alternative source for improving wheat FHB resistance.     

Identification of quantitative trait loci underlying milling quality of rice (Oryza sativa) grains

Milling quality of rice grains is important to both producers and consumers. In this study, quantitative trait loci (QTLs) controlling brown rice rate (BR), milled rice recovery (MR) and head rice recovery (HR) were analysed by composite interval mapping over 2 years using 98 backcross inbred lines (BILs). A total of 12 QTLs for the three traits were detected, of which five were for BR, four for MR and three for HR. The proportion of phenotypic variation explained by individual QTLs ranged from 7.5 to 19.9%, and additive effects contributed by a single QTL accounted for 0.46 to 2.34% of the variation. QTL‐by‐environment interactions were observed by comparing QTL mapping of the same population grown in two consecutive years. Three of five QTLs for BR and two of four QTLs for MR were detected in 2 years, and all three QTLs for HR were detected in 1 year only. BR was significantly correlated with MR, and all four QTLs of MR were located in the same regions as those of BR. This indicated that QTLs for highly correlated traits could often be detected in the same interval.