Identification of QTLs for the resistance to rice stripe virus in the <Emphasis Type="Italic">indica</Emphasis> rice variety Dular

The indica variety Dular has a high level of resistance to rice stripe virus (RSV). We performed quantitative trait locus (QTL) analysis for RSV resistance using 226 F₂ clonal lines at the seedling stage derived from a cross between the susceptible japonica variety Balilla and the resistant indica variety Dular with two evaluation criteria, infection rate (IR) and disease rating index (DRI). The experiments were performed in both 2004 and 2005. Based on IR, three putative QTLs were detected and had consistent locations in the 2 years, one QTL was detected in the RM7324–RM3586 interval on chromosome 3. The other two QTLs were linked and located in the RM287–RM209 and RM209–RM21 intervals on the long arm of chromosome 11, and accounted for 87.8–57.8% of the total phenotypic variation in both years. Based on DRI, three putative QTLs were also detected and had consistent locations in both years. One of them was located in the RM1124–SSR20 interval on the short arm of chromosome 11, while the other two linked QTLs had the same chromosomal locations on chromosome 11 as those detected by IR, and accounted for 55.7–42.9% of total phenotypic variation in both years. In comparison to the mapping results from previous studies, one of the two linked QTLs had a chromosomal location that was similar to Stv-b ⁱ , an important RSV resistance gene, while the other appeared to be a newly reported one.     

Fine mapping of a major quantitative trait locus, <Emphasis Type="Italic">qFLL6.2</Emphasis>, controlling flag leaf length and yield traits in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Fine mapping of a quantitative trait locus, qFLL6.2, controlling flag leaf length (FLL) and yield traits in rice was conducted using four sets of near isogenic lines (NILs) that were developed from a common residual heterozygote at F₇ generation of the indica rice cross Zhenshan 97/Milyang 46. Each of the NIL sets consisted of 40 lines that are S₁ progenies of ten maternal homozygotes, ten paternal homozygotes, and 20 heterozygotes differing in a portion of the 1.19-Mb interval RM3414–RM6917 on the short arm of rice chromosome 6. Analysis of phenotypic differences among the three genotypic groups in each NIL set delimited qFLL6.2 to a 62.1-kb region flanked by simple sequence repeat marker RM3414 and sequence-tagged site marker Si2944. This QTL explained 52.73% of the phenotypic variance, and the Zhenshan 97 allele increased FLL by 2.40 cm. Based on data collected from homozygous lines of three of the NIL sets, qFLL6.2 was shown to have major effects on all the three yield traits analyzed, including the number of spikelets per panicle, the number of filled grains per panicle, and grain weight per panicle. A comparison of the different groups revealed that the effect of qFLL6.2 was highly consistent across different genetic backgrounds and environments, providing a good candidate for map-based cloning and investigating the source–sink relationship in rice.     

Mapping quantitative trait loci for awnness and yield component traits in isogenic lines derived from an Oryza sativa / O. rufipogon cross

An advanced backcross line, HR9118, was produced from a single plant of BC₂F₃ families derived from a cross between Oryza rufipogon Griff. (IRGC 105491) as a donor parent and the O. sativa subsp. japonica cv. Hwaseongbyeo as a recurrent parent. Although HR9118 resembled Hwaseongbyeo, several traits were different from those of Hwasoengbyeo, including days to heading, plant height, and awn. These differences between Hwasongbyeo and HR9118 could be attributed to introgressed O. rufipogon chromosome segments into HR9118. Introgression analysis using 460 SSR markers revealed that three O. rufipogon-specific chromosome segments were detected in HR9118 genome. F_2:3 populations derived from the cross between Hwaseongbyo and HR9118, consisting of 340 F₂ plants and 137 F₃ lines, were used to map and characterize QTLs for 12 traits. QTL analysis identified a total of 17 QTLs in the F_2:3 populations. Of these, seven QTLs were shared by the F₂ and F₃ populations, whereas the other ten QTLs were identified only in the F₃ population. In seven (41.2%) QTLs identified in this study, the O. rufipogon-derived alleles contributed desirable agronomic effects despite the overall undesirable characteristics of the wild phenotype. Each of three O. rufipogon introgressed segments contained multiple QTLs, indicating linkage and/or pleotropic effects. A cluster of eight QTLs was detected on chromosome 8 including a major QTL for awn. Substitution mapping using F₂ population indicated that awn8 was located within an interval between two SSR makers RM23326 and RM23356 which are 590 kb apart. SSR markers tightly linked to QTLs for yield components detected in this study will facilitate cloning of the gene underlying this QTL as well as marker-assisted selection for variation in grain weight in an applied breeding program.     

Genetic analysis of the fiber quality and yield traits in <Emphasis Type="Italic">G. hirsutum</Emphasis> background using chromosome segments substitution lines (CSSLs) from <Emphasis Type="Italic">Gossypium barbadense</Emphasis>

Developing chromosome segments substitution lines (CSSLs) is an effective method for broadening the cotton germplasm resource, and improving the fiber quality and yield traits. In this study, the 1054 F₂ individual plants and 116 F_2:3 lineages were generated from the two parents of MBI9749 and MBI9915 selected from BC₅F_3:5 lines which originated from hybridization of CCRI36 and Hai1, and advanced backcrossing and repeated selfing. Genotypes of the parents and F₂ population were analyzed. The results showed that 19 segments were introgressed for MBI9749 and 12 segments were introgressed for MBI9915, distributing on 17 linkage groups. The average background recovery rate to the recurrent parent CCRI36 was 96.70% for the two parents. An average of 16.46 segments was introgressed in F₂ population. The average recovery rate of 1054 individual plants was 96.85%, and the mean length of sea island introgression segments was 157.18 cM, accounting for 3.15% of detection length. QTL mapping analysis detected 22 QTLs associated with fiber quality and yield traits in the F₂ and F_2:3 populations. These QTLs distributed on seven chromosomes, and the phenotypic variation was explained ranging from 1.20 to 14.61%. Four stable QTLs were detected in F₂ and F_2:3 populations, simultaneously. We found that eight QTLs were in agreement with the previous research. Six QTL-clusters were identified for fiber quality and yield traits, in which five QTL-clusters were on chromosome20. The results indicated that most of QTL-clusters always improve the fiber quality and have negative additive effect for yield related traits. This study demonstrated that CSSLs provide basis for fine mapping of the fiber quality and yield traits in future, and could be efficiently used for pyramiding favourable alleles to develop the new germplasms for breeding by molecular marker-assisted selection.     

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.     

QTL analysis for thousand-grain weight under terminal drought stress in bread wheat (<Emphasis Type="Italic">Triticum</Emphasis><Emphasis Type="Italic">aestivum</Emphasis> L.)

Grain yield under post-anthesis drought stress is one of the most complex traits, which is inherited quantitatively. The present study was conducted to identify genes determining post-anthesis drought stress tolerance in bread wheat through Quantitative Trait Loci (QTLs) analysis. Two cultivated bread wheat accessions were selected as parental lines. Population phenotyping was carried out on 133 F_2:3 families. Two field experiments and two experiments in the greenhouse were conducted at IPK-Gatersleben, Germany with control and post-anthesis stress conditions in each experiment. Thousand-grain weight was recorded as the main wheat yield component, which is reduced by post-anthesis drought stress. Chemical desiccation was applied in three experiments as simulator of post-anthesis drought stress whereas water stress was applied in one greenhouse experiment. Analysis of variance showed significant differences among the F_2:3 families. The molecular genetic linkage map including 293 marker loci associated to 19 wheat chromosomes was applied for QTL analysis. The present study revealed four and six QTLs for thousand-grain weight under control and stress conditions, respectively. Only one QTL on chromosome 4BL was common for both conditions. Five QTLs on chromosomes 1AL, 4AL, 7AS, and 7DS were found to be specific to the stress condition. Both parents contributed alleles for drought tolerance. Taking the known reciprocal translocation of chromosomes 4AL/7BS into account, the importance of the short arms of homoeologous group 7 is confirmed for drought stress.     

Mapping of QTLs detected in a <Emphasis Type="Italic">Brassica napus</Emphasis> DH population for resistance to <Emphasis Type="Italic">Sclerotinia sclerotiorum</Emphasis> in multiple environments

Sclerotinia stem rot, caused by the fungus Sclerotinia sclerotiorum, is one of the most devastating diseases of rapeseed (Brassica napus L.) in China. The two major factors limiting the development of disease resistance are (1) the absence of accessions with complete resistance and (2) the lack of a single method that can be widely applied to assess tolerance—even though accessions with differential tolerance to S. sclerotiorum have been identified in China. In the study reported here, we have used one doubled haploid (DH) population consisting of 72 lines, which was derived from the F₁ generation of a cross between a partially resistant line (DH821) and a susceptible line (DHBao604), to identify quantitative trait loci (QTLs) involved in the resistance to S. sclerotiorum. Three inoculation methods, namely, mycelial toothpick inoculation (MTI), mycelial plug inoculation (MPI), and infected petal inoculation (IPI), were used to assess resistance at the adult plant stage. A genetic linkage map with 20 linkage groups covering 1746.5 cM, with an average space of 6.93 cM, was constructed using a total of 252 molecular markers, including 91 simple sequence repeats, 72 randomly amplified polymorphic DNA, 86 sequence-related amplified polymorphisms, two restriction fragment length polymorphisms, and one expressed sequence tag. Composite interval mapping identified ten, one and ten QTLs using MTI, MPI and IPI methods, respectively, at a LOD > 2.5. One QTL was detected in linkage group N12 by MTI in 2004 and 2005 and by IPI in 2005. Another QTL was detected in linkage group N3 and N4 by MPI in 2006 and 2007. There was one common QTL detected by MTI in 2005 and by MPI in 2006. These results provide information on the genetic control of resistance to S. sclerotiorum in oilseed rape.     

Participatory selection assisted by DNA markers for enhanced drought resistance and productivity in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

In this study, a F₂ 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 F₂ 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 (F₃) 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 F₂ plants were forwarded to F₅ 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 F₆, 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.     

Identification of QTLs for resistance to anthracnose to two <Emphasis Type="Italic">Colletotrichum</Emphasis> species in pepper

Pepper (Capsicum spp.) anthracnose caused by Colletotrichum spp. is a serious disease damaging pepper production in Asian monsoon regions. For QTL mapping analyses of anthracnose resistance, an introgression BC₁F₂ population was made by interspecific crosses between Capsicum annuum ‘SP26’ (susceptible recurrent parent) and Capsicum baccatum ‘PBC81’ (resistant donor). Both green and red fruits were inoculated with C. acutatum ‘KSCa-1’ and C. capsici ‘ThSCc-1’ isolates and the disease reactions were evaluated by disease incidence, true lesion diameter, and overall lesion diameter. On the whole, distribution of anthracnose resistance was skewed toward the resistant parent. It might indicate that one or two major QTLs are present. The introgression map consisting of 13 linkage groups with a total of 218 markers (197 AFLP and 21 SSR), covering a total length of 325 cM was constructed. Composite interval mapping analysis revealed four QTLs for resistance to ‘KSCa-1’ and three QTLs for ‘ThSCc-1’ isolate, respectively. Interestingly, the major QTLs (CaR12.2 and CcR9) for resistance to C. acutatum and C. capsici, respectively, were differently positioned but there were close links between the minor QTL CcR12.2 for C. capsici and major QTL CaR12.2 as well as the minor QTL CaR9 for C. acutatum and major QTL CcR9. These results will be helpful for marker-assisted selection and pyramiding two different anthracnose-resistant genes in commercial pepper breeding.     

Identification of quantitative trait loci for bruchid (<Emphasis Type="Italic">Callosobruchus maculatus</Emphasis>) resistance in black gram [<Emphasis Type="Italic">Vigna mungo</Emphasis> (L.) Hepper]

An inter-subspecific mapping population was generated by crossing V. mungo var. mungo (cv. TU 94-2, bruchid susceptible) and V. mungo var. silvestris (bruchid resistant). About 37.8% of the bruchid completed their lifecycle on seeds of V. mungo var. silvestris compared with 100% on the susceptible variety TU 94-2. The total developmental period of C. maculatus on Vigna mungo var. silvestris was considerably extended (88 days as compared with 34 days on TU 94-2). A genetic linkage map constructed using recombinant inbred lines (RILs) in F₉ generation with 428 markers [86 random amplified polymorphic DNA (RAPD), 47 simple sequence repeat (SSR), 41 inter-SSR (ISSR), 254 amplified fragment length polymorphism (AFLP)] was used for QTL detection. One hundred four individuals were used for detection of QTLs associated with bruchid resistance. The RILs exhibited a high level of variation in percentage adult emergence (0–100%) and developmental period (0–105 days). Two QTLs, Cmrae1.1 and Cmrae1.2, were identified for percentage adult emergence, on linkage group (LG) 3 and 4, respectively. For developmental period, six QTLs were identified, with two QTLs (Cmrdp1.1 and Cmrdp1.2) on LG 1, three QTLs (Cmrdp1.3, Cmrdp1.4, and Cmrdp1.5) on LG 2, and one QTL (Cmrdp1.6) on LG 10.     

Fine mapping of <Emphasis Type="Italic">Rf3</Emphasis> and <Emphasis Type="Italic">Rf4</Emphasis> fertility restorer loci of WA-CMS of rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) and validation of the developed marker system for identification of restorer lines

The Wild Abortive (WA) system is the major cytoplasmic male sterility (CMS) source for hybrid rice production in indica rice and its fertility restoration is reported to be controlled by two major loci viz. Rf3 on chromosome 1 and Rf4 on chromosome 10. With the availability of the rice genome sequence, an attempt was made to fine map, develop candidate gene based markers for Rf3 and Rf4 and validate the developed marker system in a set of known restorer lines. Using polymorphic markers developed from microsatellite markers and candidate gene based markers from Rf3 and Rf4 loci, local linkage maps were constructed in two mapping populations of ~1,500 F₂ progeny from KRH2 (IR58025A/KMR3R) and DRRH2 (IR68897A/DR714-1-2R) hybrids. QTLs and their interactions for fertility restoration in Rf3 and Rf4 loci were identified. The identified QTL in both mapping populations together explained 66–72 % of the phenotypic variance of the trait suggesting their utility in developing a marker system for identification of fertility restorers for WA-CMS. Sequence comparison of the two candidate genes from the Rf3 and Rf4 regions in male sterile (A) and restorer (R) lines showed 2–3 bp indels and a few substitutions in the Rf3 region and indels of 327 and 106 bp in the Rf4 region respectively. The marker system identified in the present study was validated in 212 restorers and 34 maintainers along with earlier reported markers for fertility restoration of WA-CMS. Together DRCG-RF4-14 and DRCG-RF4-8 for the Rf4 locus and DRRM-RF3-5/DRRM-RF3-10 for the Rf3 locus showed a maximum efficiency of 92 % for identification of restorers.     

Fine mapping of major QTLs for alkaline tolerance at the seedling stage in maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) through genetic linkage analysis combined with high-throughput DNA sequencing

Exploiting genes and quantitative trait loci (QTLs) related to maize (Zea mays L.) alkaline tolerance is helpful for improving alkaline resistance. To explore the inheritance of maize alkaline tolerance at the seedling stage, a mapping population comprising 151 F_2:3 lines derived from the maize cross between Zheng58, tolerant to alkaline, and Chang7-2, sensitive to alkaline, was used to establish a genetic linkage map with 200 SSR loci across the 10 maize linkage groups, with an average interval of 6.5 cM between adjacent markers. QTLs for alkaline resistant traits of alkaline tolerance rating (ATR), germination rate (GR), relative conductivity (RC), weight per plant (WPP) and proline content (PC) were detected. The obtained results were as follows: Five QTLs on chromosomes 2, 5 and 6 (GR and WPP: chr. 2; PC and ATR: chr. 5; and RC: chr. 6) were mapped. For precise mapping of the QTLs related to alkaline resistance, two bulked deoxyribonucleic acid (DNA) pools were constructed using individual DNAs from the most tolerant 30 F₂ individuals and the most sensitive 30 F₂ individuals according to the ATR and used to establish a high density map of SLAF markers strongly associated with the ATR by specific locus amplified fragment sequencing (SLAF-Seq) combined with super bulked segregant analysis (superBSA). One marker-intensive region involved three SLAFs at 296,000–6,203,000 bp on chromosome 5 that were closely related to the ATR. Combined with preliminary QTL mapping with superBSA, two major QTLs on chromosome 5 associated with alkaline tolerance at the maize seedling stage were mapped to marker intervals of dCap-SLAF31521 and dCap-SLAF31535 and phi024 and dCap-SLAF31521, respectively. These QTL regions involved 9 and 75 annotated genes, respectively. These results will be helpful for improving maize alkaline tolerance at the seedling stage by marker-assisted selection programs and will be useful for fine mapping QTLs for maize breeding.     

Stay-green expression in early generation sorghum [<Emphasis Type="Italic">Sorghum bicolor</Emphasis> (L.) Moench] QTL introgression lines

Reduced leaf senescence (stay-green) has been demonstrated to improve tolerance of post-flowering moisture stress in grain sorghum. A number of quantitative trait loci (QTLs) associated with stay-green have been identified in sorghum, to facilitate transfer of this trait into adapted genetic backgrounds. This study reports initial evaluations, in both well watered and post-flowering stress environments, following partial introgression (BC₂F₃/BC₁F₄ generations) of four stable stay-green QTLs (StgB, Stg1, Stg3 and Stg4) from donor parent B35 to senescent variety R 16. The majority of the introgression lines had higher leaf chlorophyll levels at flowering (a distinctive trait of the donor parent) and a greater percentage green leaf area during the latter part of grain filling, than did R 16, indicating that the stay-green QTLs were expressed phenotypically in the R 16 background. None of the QTL introgression lines achieved the same level of stay-green as B35, however. Maintenance of a greater relative green leaf area during the latter half of grain filling was related to a greater relative grain yield in two of three post-flowering moisture deficit environments in which the materials were evaluated (r ² = 0.34 in 2004–2005 and r ² = 0.76 in 2005–2006), as was a direct measure of leaf chlorophyll in one of the post-flowering stress environments in which this was measured (r ² = 0.42, P < 0.05). Thus the study provided useful evidence that the marker-assisted backcross transfer of stay-green QTLs from B35 into an adapted, but senescent background has the potential to enhance tolerance of post-flowering drought stress in sorghum.     

A major QTL associated with preharvest sprouting in rapeseed (<Emphasis Type="Italic">Brassica napus</Emphasis> L.)

Preharvest sprouting (PHS) is one of the most important factors affecting the cereal production worldwide, in regions characterized by rainfall and high humidity during harvest season. It is sometimes a problem in rapeseed (Brassica napus L.), especially in production of commercial F₁ hybrids. To detect quantitative trait loci (QTL) controlling PHS, a F₂ population consisting of 269 F_2:3 lines was created from the cross between a PHS-tolerant line (117AB) and a PHS-susceptible line (7,605). A linkage map was constructed using 35 Simple Sequence Repeat markers and 242 Amplified Fragment Length Polymorphism markers. PHS was measured as a percentage of sprouted seeds on the mother plant, 7 days after physiological maturity. Five putative QTLs for PHS were detected and located on LG2 (N11) and LG7 (N3), respectively. Phenotypic variance explained by each QTL ranged from 4.11 to 50.78% and the five putative QTLs explained about 75.63% of the total phenotypic variance. A major QTL was identified on LG2 (N11) flanked by P3C4180 and C6C13160, which explained 50.78% of the total phenotypic variance. Meanwhile, we detected four significant epistatic interactions with a total contribution of 17.16% of the total phenotypic variance.     

Mapping QTLs for grain quality using an introgression line population from a cross between <Emphasis Type="Italic">Oryza sativa</Emphasis> and <Emphasis Type="Italic">O. rufipogon</Emphasis>

Quantitative trait loci (QTL) associated with four milling recovery properties, two chemical properties, six paste properties of grain, and six textural parameters of cooked rice were identified using an introgression line (IL) population of rice developed from an interspecific cross over two years. The IL population consisted of 121 lines from a cross between wild rice (O. rufipogon Griff.) and a japonica cultivar. A total of 28 QTLs were identified for the 14 traits using inter mapping. Of these, 10 were significant over two years indicating that these QTLs are stable across years and environments. For eight (21%) of the QTLs identified, the O. rufipogonderived alleles contributed a desirable effect on amylose content, protein content, minimum viscosity, final viscosity, and consistency. Among these, pc3 for protein content and ac7 for amylose content were significant in both years and showed an R² value of 25.5 and 30.9%, respectively. The markers closely associated with these useful alleles can be used to trace the inheritance of specific chromosome segments in the IL population and also offer a starting point for map-based cloning of genes underlying these traits.     

Genetic analysis and QTL mapping of fruit-related traits in wax gourd (<Emphasis Type="Italic">Benincasa hispida</Emphasis>)

As an important fruit vegetable, fruit-related traits have become one of the breeding hotspots of wax gourd (Benincasa hispida). The fruit traits have an important role on the quality and yield of wax gourd, and QTL mapping of these traits will provide solid basis for fruit character improvement as well as high-yield breeding. In this study, the inheritance of four fruit-related traits, including fruit weight (FW), fruit length (FL), fruit diameter (FD) and flesh thickness (FT), was analyzed. All the frequency distribution of the four traits in an F₂ population showed a single peak skewed distribution, which proved them to be quantitative. Subsequently, based on the high-density genetic map using 140 F₂ individuals, nine QTLs associated with the four traits were detected on chromosome 3, 4, 5, 6, 9, 10 and 11. Four of the nine QTLs had major effect, which were responsible for more than 10.0% of phenotypic variance. Furthermore, the major QTLs of FW, FD and FT shared similar location intervals, which implied that this location might contain some pleiotropic genes. This is the first report on QTL mapping of quantitative trait in wax gourd, which plays an important role for fine mapping of these important fruit traits.     

Identification and mapping of quantitative resistance to late blight (<Emphasis Type="Italic">Phytophthora infestans</Emphasis>) in <Emphasis Type="Italic">Solanum habrochaites</Emphasis> LA1777

Late blight (Phytophthora infestans) can have devastating effects on tomato production over the whole world. Most of the commercial cultivars of tomato, Solanum lycopersicum, are susceptible. Qualitative and quantitative resistance has been described in wild relatives of tomato. In general qualitative resistance can more easily be overcome by newly evolved isolates. Screening of three S. habrochaites accessions (LA1033, LA2099 and LA1777) through a whole plant assay showed that accession LA1777 had a good level of resistance to several isolates of P. infestans. To explore the potential in this wild species, an introgression line (IL) population of S. habrochaites LA1777 was used to screen individual chromosome regions of the wild species by a detached leaf assay. Two major isolates (T_1,2 and T_1,2,4) were used and two parameters were measured: lesion size (LS), and disease incidence (DI). Substantial variation was observed between the individual lines. QTLs were identified for LS but not for DI. The presence of five QTLs derived from LA1777 (Rlbq4a, Rlbq4b, Rlbq7, Rlbq8 and Rlbq12) results in unambiguous higher levels of resistance. All QTLs co-localized with previously described QTLs from S. habrochaites LA2099 except QTL Rlbq4b, which is therefore a novel QTL.     

Identification of QTLs associated with heat tolerance at the heading and flowering stage in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

The ongoing rise in temperatures caused by global climate change is a critical climatic risk factor for rice production, and enhancing rice heat tolerance is an area of particular research interest. A recombinant inbred line (RIL) mapping population was developed from heat sensitive, rice cultivar IAPAR-9 crossed with heat tolerant, Liaoyan241. RIL and parental lines were exposed to high temperature at the heating and flowering stage in experiments in 2014 and 2015. As indicators of heat tolerance, the seed setting rate under natural (NS) and heat stress (HTS) conditions were measured, and the reduction rate of seed set (RRS) was calculated. Quantitative trait loci (QTL) analysis revealed eleven heat tolerance QTLs located on chromosomes 1, 3, 4, 5, and 6. Single QTL contribution rates were 4.75–13.81% and effect values were ? 5.98 to 5.00. Four major QTLs (qNS1, qNS4, qNS6, and qRRS1) were stable detected in different environments in both years. Thirteen QTLs with epistatic interactions and nine QTLs with environmental interactions were also detected. Major QTLs were all involved in epistatic and environmental interactions. Three QTLs from the SSR marker interval RM471 to RM177 region of chromosome 4 (qNS4, qHTS4, and qRRS4) were all involved in epistatic and environmental interactions and contributed to phenotypic variation, indicating that this region constituted a major QTL hotspot. The major QTL for heat tolerance identified in this study will aid in breeding tolerant cultivars and facilitating investigation of the molecular underpinnings of heat tolerance in rice.     

Confirmation of quantitative trait loci for resistance to multiple-HG types of soybean cyst nematode (<Emphasis Type="Italic">Heterodera glycines</Emphasis> Ichinohe)

Genetic analysis of resistance of plant introduction (PI) 438489B to soybean cyst nematode (SCN) have shown that this PI is highly resistant to many SCN HG types. However, validation of the previously detected quantitative trait loci (QTL) has not been done. In this study, 250 F_2:3 progeny of a Magellan (susceptible) × PI 438489B (resistant) cross were used for primary genetic mapping to detect putative QTL for resistance to five SCN HG types. QTL confirmation study was subsequently conducted using F_6:7 recombinant inbred lines (RILs) derived from the same cross. Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were employed for molecular genotyping. Interval mapping (IM), permutation tests, cofactor selection, and composite interval mapping (CIM) were performed to identify and map QTL. Results showed that five QTL intervals were associated with resistance to either multiple- or single-HG types of SCN. Among these, two major QTL for resistance to multiple-SCN HG types were mapped to chromosomes (Chr.) 8 and 18, consistent with the known rhg1 and Rhg4 locations. The other QTL were mapped to Chr. 4. The results of our study confirmed earlier reported SCN resistance QTL in this PI. Moreover, SSR and SNP molecular markers tightly linked to these QTL can be useful for the near-isogenic lines (NILs) development aiming to fine-mapping of these QTL regions and map-based cloning of SCN resistance candidate genes.     

Mapping of quantitative trait loci controlling powdery mildew resistance in Mungbean (<Emphasis Type="Italic">Vigna radiata</Emphasis> (L.) Wilczek)

Powdery mildew disease in mungbean is caused by the fungus, Erysiphe polygoni D.C. We identified two quantitative trait loci (QTLs) controlling resistance to the disease in a RIL population of 190 F₇ lines. The population was developed from the cross between a susceptible cultivar, “Kamphaeng Saen 1” and a resistant line, “VC6468-11-1A”. Reaction to the disease was evaluated for resistance in field and greenhouse conditions. Results from analysis of variance revealed that 15 SSR loci on three linkage groups (LG) associated with the resistance. Composite interval mapping consistently identified two QTLs on two LGs, qPMR-1 and qPMR-2, conferring the resistance. qPMR-1 and qPMR-2 accounted for 20.10 and 57.81% of the total variation for plant response to the disease, respectively. Comparison based on common markers used in our and previous studies suggested that qPMR-2 is possibly the same as the major QTL reported earlier using another resistant source. The SSR markers flanking and closely linked to qPMR-1 (CEDG282 and CEDG191) and qPMR-2 (MB-SSR238 and CEDG166) are useful for marker-assisted selection for mungbean resistance to powdery mildew.