Inclusive Composite Interval Mapping Research Articles

Genetic determinants for agronomic and yield-related traits localized on a GBS-SNP linkage map from a japonica x indica cross in rice

Rice is an important cereal for human consumption. Identification of QTLs for important agronomic traits with high resolution is essential to the identification of genes and marker-assisted breeding to improve rice productivity. A genotyping by sequencing (GBS)-based high-resolution SNP linkage developed in a recombinant inbred lines (RIL) population of a japonica (Bengal) × indica (Pokkali) cross was used for QTL analysis of traits such as days to heading, plant height, panicle length, flag leaf length, 1000 kernel weight, number of unfilled grains, number of filled grains, grain width, grain length, and awns using interval mapping and inclusive composite interval mapping approaches. Among the 102 additive QTLs identified for the ten traits, 23 QTLs were major effect QTLs. A chromosomal region flanking the sd-1 gene colocalized the QTLs for plant height, panicle length, and flag leaf length, suggesting possible pleiotropic effects on the expression of these traits. Our study not only reduced confidence intervals of previously identified QTLs but also validated several known genes for heading date (Hd1), panicle length (APO1), grain width (GW2, GW5) and awn length (An-1). Furthermore, candidate genes for several agronomic traits were identified. Annotations of genes within novel QTLs for yield-related traits revealed that RCN4 (LOC_Os06g45460), expansin precursor (LOC_Os02g51040), and RGB1 (LOC_Os03g46650) are promising candidates for yield enhancement. Our study provided genetic insights into the important agronomic and yield enhancing traits through identification of QTLs and candidate genes for future validation and molecular breeding to improve rice yield potential.

Identification and validation of genetic loci for tiller angle in bread wheat.

Two major QTL for tiller angle were identified on chromosomes 1AL and 5DL, and TaTAC-D1might be the candidate gene for QTA.caas-5DL. An ideal plant architecture is important for achieving high grain yield in crops. Tiller angle (TA) is an important factor influencing yield. In the present study, 266 recombinant inbred lines (RILs) derived from a cross between Zhongmai 871 (ZM871) and its sister line Zhongmai 895 (ZM895) was used to map TA by extreme pool-genotyping and inclusive composite interval mapping (ICIM). Two quantitative trait loci (QTL) on chromosomes 1AL and 5DL were identified with reduced tiller angle alleles contributed by ZM895. QTA.caas-1AL was detected in six environments, explaining 5.4-11.2% of the phenotypic variances. The major stable QTL, QTA.caas-5DL, was identified in all eight environments, accounting for 13.8-24.8% of the phenotypic variances. The two QTL were further validated using BC1F4 populations derived from backcrosses ZM871/ZM895//ZM871 (121 lines) and ZM871/ZM895//ZM895 (175 lines). Gene TraesCS5D02G322600, located in the 5DL QTL and designated TaTAC-D1, had a SNP in the third exon with 'A' and 'G' in ZM871 and ZM895, respectively, resulting in a Thr169Ala amino acid change. A KASP marker based on this SNP was validated in two sets of germplasm, providing further evidence for the significant effects of TaTAC-D1 on TA. Thus extreme pool-genotyping can be employed to detect QTL for plant architecture traits and KASP markers tightly linked with the QTL can be used in wheat breeding programs targeting improved plant architecture.

Genetic mapping of physiological traits associated with terminal stage drought tolerance in rice

BackgroundDrought during reproductive stage is among the main abiotic stresses responsible for drastic reduction of grain yield in rainfed rice. The genetic mechanism of reproductive stage drought tolerance is very complex. Many physiological and morphological traits are associated with this stress tolerance. Robust molecular markers are required for detection and incorporation of these correlated physiological traits into different superior genetic backgrounds. Identification of gene(s)/QTLs controlling reproductive stage drought tolerance and its deployment in rainfed rice improvement programs are very important.ResultsQTLs linked to physiological traits under reproductive stage drought tolerance were detected by using 190 F7 recombinant inbred lines (RIL) mapping population of CR 143–2-2 and Krishnahamsa. Wide variations were observed in the estimates of ten physiological traits studied under the drought stress. The RIL population was genotyped using the bulk- segregant analysis (BSA) approach. A total of 77 SSR polymorphic markers were obtained from the parental polymorphisms survey of 401 tested primers. QTL analysis using inclusive composite interval mapping detected a total of three QTLs for the physiological traits namely relative chlorophyll content (qRCC1.1), chlorophyll a (qCHLa1.1), and proline content (qPRO3.1) in the studied RIL population. The QTL, qPRO3.1 is found to be a novel one showing LOD value of 13.93 and phenotypic variance (PVE) of 78.19%. The QTL was located within the marker interval of RM22-RM517 on chromosome 3. Another novel QTL, qRCC1.1 was mapped on chromosome 1 at a distance of 142.8 cM and found to control relative chlorophyll content during terminal drought stress. A third novel QTL was detected in the population that controlled chlorophyll a content (qCHLa1.1) under the terminal stress period. The QTL was located on chromosome 1 at a distance of 81.8 cM and showed 64.5% phenotypic variation.ConclusionsThe three novel QTLs, qRCC1.1, qCHLa1.1 and qPRO3.1 controlling relative chlorophyll content, chlorophyll a and proline content, respectively were identified in the mapping population derived from CR 143–2-2 and Krishnahamsa. These 3 QTLs will be useful for enhancement of terminal drought stress tolerance through marker-assisted breeding approach in rice.

QTL Mapping for Agronomic and Adaptive Traits Confirmed Pleiotropic Effect of mog Gene in Black Gram [Vigna mungo (L.) Hepper

Organ size and architecture of plants are important traits affecting crop yield and agronomic practices. An induced mutant, multiple-organ gigantism (MOG), of black gram (Vigna mungo) has been obtained, which shows gigantic leaves, fruit, seed, and architecture (plant height) but lower number of pods per plant. These traits are a pleiotropic effect of a single recessive gene, mog. In this study, we investigated variation of 16 agronomic and adaptive traits in a recombinant inbred line (RIL) population derived from a cross between the MOG mutant (V. mungo var. mungo) and wild black gram (V. mungo var. silvestris) accession TC2210 and identified quantitative trait loci (QTLs) controlling those traits to gain a better understanding of the effect of the mog gene on breeding. The results showed that most of the traits (100-seed weight, leaf size, and plant height) showed moderate narrow-sense heritability (h2) (45–65%), while pod size and seed length (SDL) showed high h2 (>75%) and pod dehiscence (shattering), and seed width (SDW) and days to flowering showed low h2 (<35%). The QTLs for the traits were mapped onto a high-density linkage map developed for the RIL population. Inclusive composite interval mapping identified 42 QTLs in total for the 16 traits with number of QTLs per trait ranging from one to six. Major QTLs for the MOG phenotypes were clustered on linkage group (LG) 6, confirming the pleiotropic effect of the mog gene. Effect of the mog gene/QTL for the MOG phenotypic variations was not high, ranging from about 15% in plant height to 40% in leaf size. For 100-seed weight, which is the most interesting trait, the mog gene/QTL contributed about 30% of the total trait variation and showed an additive effect of only 0.51 g, which is only about 1.5-fold higher than that of the other five QTLs detected for this trait. These results indicated that mog gene expression is highly affected by environment and the effect of the gene toward organ size and plant height is not extraordinarily high. Implications of the findings of this study and exploiting of the MOG mutant in breeding were also discussed.

Quantitative Trait Locus Analysis of Protein and Oil Content in Response to Planting Density in Soybean (Glycine max [L.] Merri.) Seeds Based on SNP Linkage Mapping.

Soybean varieties suitable for high planting density allow greater yields. However, the seed protein and oil contents, which determine the value of this crop, can be influenced by planting density. Thus, it is important to understand the genetic basis of the responses of different soybean genotypes to planting density. In this study, we quantified the protein and oil contents in a four-way recombinant inbred line (FW-RIL) soybean population under two planting densities and the response to density. We performed quantitative trait locus (QTL) mapping using a single nucleotide polymorphism (SNP) linkage map generated by inclusive composite interval mapping. We identified 14 QTLs for protein content and 17 for oil content at a planting density of 2.15 × 105 plant/ha (D1) and 14 QTLs for protein content and 20 for oil content at a planting density 3.0 × 105 plant/ha (D2). Among the QTLs detected, two oil-content QTLs was detected at both plant densities. In addition, we identified 38 QTLs for the responses of protein and oil contents to planting density. Of the QTLs detected, 70 were identified in previous studies, while 33 were newly identified. Fourty-five QTLs accounted for over 10% of the phenotypic variation of the corresponding trait, based on 23 QTLs at a marker interval distance of ~600 kb detected under different densities and with the responses to density difference. Pathway analysis revealed four candidate genes involved in protein and oil biosynthesis/metabolism. These results improve our understanding of the genetic underpinnings of protein and oil biosynthesis in soybean, laying the foundation for enhancing protein and oil contents and increasing yields in soybean.

QTL for the iron and zinc contents of the milled grains of a doubled-haploid rice (Oryza sativa L.) population grown over two seasons

Identifying iron- and zinc-related quantitative trait loci (QTL) with consistent effects across environments and genetic backgrounds is necessary to develop rice varieties with high grain iron content (GIC) and grain zinc content (GZC). In this work, a doubled haploid population was developed through a cross between the Korean japonica cultivars Goami 2 and Hwaseonchal and phenotyped during the 2018 wet season (POP2018) and 2019 wet season (POP2019). The milled rice grains of POP2018 and POP2019 were used to identify GIC- and GZC-related QTL that was consistent between years. Digenic interactions and genes that affected GIC and GZC were also identified. Paired sample t test revealed that the GIC of POP2018 was not significantly different from that of POP2019 (t = 0.24, p =0.81), whereas the GZC of POP2018 was significantly different from that of POP2019 (t = − 4.35, p =0.00). Three moderate-effect (phenotypic variance [PVE] < 10.00%) GIC- and GZC-related QTL that were consistent between POP2018 and POP2019 were identified through inclusive composite interval mapping: qFe9, qFe11, and qZn7. All three QTL originated from the inferior parent Hwaseonchal. Epistasis analysis revealed that the GIC and GZC of POP2018 and POP2019 were affected by 79 significant digenic interactions with moderate and minor effects. By contrast, GZC was unaffected by digenic interactions. An interaction between loci on chromosomes 1 and 5 provided the highest contribution to the PVE (13.72%) for GIC. Candidate gene analysis revealed that 12 genes related to iron and zinc homeostasis or that require iron or zinc as ligands colocated with qFe9, qFe11, and qZn7. The QTL and epistatic regions identified here may be useful for developing rice varieties with high GIC and GZC in their milled grains.

Tagging, Mapping and Identification of the QTLs Associated With Phosphorous Utilization for Phosphorous- Limiting Soils in Tropical Maize

Phosphorus (P) deficiency is one of the major abiotic constraints leading to low maize productivity. Twenty- four SSR markers sequence information was obtained from maize databases (MaizeGDB). These SSRs were selected from targeted regions of the maize genome linked to Quantitative Trait Loci (QTLs) for Phosphorus utilization efficiency. The mapping population consisting 67 F2 maize plants, were obtained from advancing a bi-parental cross between an efficient line (L354) and an in-efficient maize line (L585). Out of 24 SSRs five identified polymorphic SSR markers were subsequently used for genotyping the 67 tagged F2 plants. Sixty seven F2:3 maize families were used for QTL localization. Inclusive composite interval mapping (ICIM) analysis identified seven QTLs associated with phosphorus utilization on chromosome 5. All the mapped QTLs were more than 5 cM from the nearest molecular marker utilized in the study. The closest mapped QTL, PeSB-5, 7 associated with shoot biomass was at 11.7 cM, from the nearest marker umc2136 on chromosome 5. Therefore, there is need to saturate the map which may prove useful to identify and test several markers near the mapped QTLs. The identified markers could serve as potential SSR markers for QTLs associated with phosphorous utilization for phosphorous- limiting soils in tropical maize.

Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice

BackgroundThe construction of genetic maps based on molecular markers is a crucial step in rice genetic and genomic studies. Pure lines derived from multiple parents provide more abundant genetic variation than those from bi-parent populations. Two four-parent pure-line populations (4PL1 and 4PL2) and one eight-parent pure-line population (8PL) were developed from eight homozygous indica varieties of rice by the International Rice Research Institute (IRRI). To the best of our knowledge, there have been no reports on linkage map construction and their integration in multi-parent populations of rice.ResultsWe constructed linkage maps for the three multi-parent populations and conducted quantitative trait locus (QTL) mapping for heading date (HD) and plant height (PH) based on the three maps by inclusive composite interval mapping (ICIM). An integrated map was built from the three individual maps and used for QTL projection and meta-analysis. QTL mapping of the three populations was also conducted based on the integrated map, and the mapping results were compared with those from meta-analysis. The three linkage maps developed for 8PL, 4PL1 and 4PL2 had 5905, 4354 and 5464 bins and were 1290.16, 1720.01 and 1560.30 cM in length, respectively. The integrated map was 3022.08 cM in length and contained 10,033 bins. Based on the three linkage maps, 3, 7 and 9 QTLs were detected for HD while 6, 9 and 10 QTLs were detected for PH in 8PL, 4PL1 and 4PL2, respectively. In contrast, 19 and 25 QTLs were identified for HD and PH by meta-analysis using the integrated map, respectively. Based on the integrated map, 5, 9, and 10 QTLs were detected for HD while 3, 10, and 12 QTLs were detected for PH in 8PL, 4PL1 and 4PL2, respectively. Eleven of these 49 QTLs coincided with those from the meta-analysis.ConclusionsIn this study, we reported the first rice linkage map constructed from one eight-parent recombinant inbred line (RIL) population and the first integrated map from three multi-parent populations, which provide essential information for QTL linkage mapping, meta-analysis, and map-based cloning in rice genetics and breeding.

Linkage Analysis and Multi-Locus Genome-Wide Association Studies Identify QTNs Controlling Soybean Plant Height.

Plant height is an important target for soybean breeding. It is a typical quantitative trait controlled by multiple genes and is susceptible to environmental influences. Here, we carried out phenotypic analysis of 156 recombinant inbred lines derived from “Dongnong L13” and “Henong 60” in nine environments at four locations over 6 years using interval mapping and inclusive composite interval mapping methods. We performed quantitative trait locus (QTL) analysis by applying pre-built simple-sequence repeat maps. We detected 48 QTLs, including nine significant QTLs detected by multiple methods and in multiple environments. Meanwhile, genotyping of all lines using the SoySNP660k BeadChip produced 54,836 non-redundant single-nucleotide polymorphism (SNP) genotypes. We used five multi-locus genome-wide association analysis methods to locate 10 quantitative trait nucleotides (QTNs), four of which overlap with previously located QTLs. Five candidate genes related to plant height are predicted to lie within 200 kb of these four QTNs. We identified 19 homologous genes in Arabidopsis, two of which may be associated with plant height. These findings further our understanding of the multi-gene regulatory network and genetic determinants of soybean plant height, which will be important for breeding high-yielding soybean.

Genetic Analysis of Agronomic Traits and Grain Iron and Zinc Concentrations in a Doubled Haploid Population of Rice (Oryza sativa L.)

The development of micronutrient dense rice varieties with good agronomic traits is one of the sustainable and cost-effective approaches for reducing malnutrition. Identification of QTLs for high grain Fe and Zn, yield and yield components helps in precise and faster development of high Fe and Zn rice. We carried out a three-season evaluation using IR05F102 x IR69428 derived doubled-haploid population at IRRI. Inclusive composite interval mapping was carried out using SNP markers and Best Linear Unbiased Estimates of the phenotypic traits. A total of 23 QTLs were identified for eight agronomic traits and grain Fe and Zn concentration that explained 7.2 to 22.0% PV. A QTL by environment interaction analysis confirmed the stability of nine QTLs, including two QTLs for Zn on chromosomes 5 and 12. One epistatic interaction for plant height was significant with 28.4% PVE. Moreover, five QTLs were identified for Fe and Zn that harbor several candidate genes, e.g. OsZIP6 on QTL qZn5.1. A number of QTLs were associated with a combination of greater yield and increased grain Zn levels. These results are useful for development of new rice varieties with good agronomic traits and high grain Zn using MAS, and identification of genetic resources with the novel QTLs for grain Zn.

Genetic analysis and gene detection of fructan content using DArT molecular markers in spring bread wheat (Triticum aestivum L.) grain

Fructans (fructo-oligosaccharides) is one of the most important carbohydrates in wheat vegetative tissues and plays a vital role in wheat grain development. One hundred and forty 'Avocet'× 'Chilero' wheat (Triticum aestivum L.) recombinant inbred lines (RILs) were phenotyped for grain fructans at Luoyang and Langzhou field sites in the 2015-2016 and 2016-2017 growing seasons and 2090 Diversity Arrays Technology (DArT) molecular marker data were used to determine genomic regions controlling fructan content. Eleven significant quantitative trait loci (QTL) for wheat fructan content were identified on chromosomes 1B, 2A, 2B, 2D, 3D, 4B, 6B, 6D, 7A, and 7B using the inclusive composite interval mapping (ICIM) method, explaining 4.08% to 27.40% of the phenotypic variance, with seven exceeding 10%. The single environment analysis identified QF.haust-6D.1 and QF.haust-7B in Luoyang, QF.haust-1B, QF.haust-2D, QF.haust-3D, and QF.haust-7B in Lanzhou, and QF.haust-1B, QF.haust-7A, and QF.haust-7B in average phenotypic performance. The multi-environment analysis identified QF.haust-2B and QF.haust-7B, which explained 21.01% and 17.39% of the phenotypic variance, respectively. The positive allele of QF.haust-2B and QF.haust-7B were all originated from Chilero. QF.haust-2B was flanked by the 3957031 and SNP1203021 markers; candidate genes for QF.haust-2B were identified by anchoring marker sequences in the IGWSC wheat genome sequence, involving a variety of biological processes, such as the regulation of ribosomes metabolism in wheat. We also constructed the physical map for wheat grain fructan QF.haust-2B and QF.haust-7B, QF.haust-7B with a physical length of 11.47 Mb between marker SNP3026392 and 3954877 and 103 genes within the segment, in which ten were related to glucose metabolism. This study provides a theoretical basis and technical support for wheat grain fructan content-related genes and molecular marker-assisted breeding.

Deploying inter-specific recombinant inbred lines to map QTLs for yield-related traits in soybean

Quantitative trait loci (QTL) mapping and analyses were conducted for yield and six yield-related traits in soybean using 184 inter-specific recombinant inbred lines (RILs) derived from a cross involving wild type (Glycine soja Sieb. and Zucc.) accession DC2008-1 and cultivated (Glycine max L. Merr.) variety DS9712. A Linkage map of 1639.55 cM length was constructed with 167 SSR markers (65.65% polymorphism) with an average marker interval of 9.82 cM. Using three years phenotypic data 34 QTLs were mapped for 7 traits using Inclusive Composite Interval Mapping approach. The number of QTLs mapped for a trait varied from year to year, however, QTLs for days-to-50% flowering (qDFF5), 100-seed weight (qHSW9-1, qHSW9-2 and qHSW19) and yield (qYLD17) were mapped consistently over the three years of testing. Identified QTLs were validated through single marker analysis in 92 germplasm lines. The study demonstrated the potential of wild type soybean to harness QTLs for yield-related traits. The identified QTLs could be utilized for genetic improvement of soybean through molecular breeding.

QTL mapping of adult plant resistance to stripe rust and leaf rust in a Fuyu 3/Zhengzhou 5389 wheat population

Stripe or yellow rust (YR) and leaf rust (LR) cause large losses in wheat production worldwide. Resistant cultivars curtail the levels of losses. The present study aimed to identify quantitative trait loci (QTL) for YR and LR resistance in 147 F2:6 recombinant inbred lines (RIL) derived from the cross Fuyu 3/Zhengzhou 5389. The RIL population and parents were genotyped with the Wheat55K single nucleotide polymorphism (SNP) array and simple sequence repeat (SSR) markers. All materials were also phenotyped for YR severity at Mianyang in Sichuan province and Baoding in Hebei province in the 2015/2016, 2016/2017, and 2017/2018 cropping seasons, and LR severity at Zhoukou in Henan province and at Baoding in 2017/2018. Eleven QTL for YR resistance and five for LR resistance were detected using inclusive composite interval mapping (IciMapping). Four of these QTL on chromosomes 1BL, 2BS, 3AL, and 5AL conferred resistance to both YR and LR. The QTL on 1BL was Lr46/Yr29, and that on 7BL might be Lr68. The QTL on chromosome 2BS was detected at a similar position to previously detected loci. QYr.hebau-3AL/QLr.hebau-3AL, QYr.hebau-5AL/QLr.hebau-5AL, QYr.hebau-7DL, QYr.hebau-4BS, QYr.hebau-6DL, and QYr.hebau-2AS are likely to be new. An SSR marker for QYr.hebau-7DL was developed and validated in a diverse wheat panel from China, suggesting effectiveness in different genetic backgrounds. These QTL with closely linked SNP and SSR markers could be useful for marker-assisted selection in wheat breeding programs targeting durable resistance to both diseases.

QTL Mapping and Genetic Analysis of Fiber Quality Traits in Hybrid Cotton

&lsquo;Ji1518&rsquo; is a new hybrid cotton variety suitable for mechanized harvesting, the two parents of &lsquo;Ji228&rsquo; and &lsquo;Ji567&rsquo; were crossed to established F2, F2:3 and F2:9 (recombinant inbred lines RILs) population. Simple sequence repeats (SSR) was performed to construct two different genetic maps based on the F2 and F2:9 populations respectively. The QTL mapping of five fiber quality traits was performed in three populations above. A genetic map was constructed by F2 population, which contained 15 loci in 4 linkage groups, with a full-length coverage of 237.10 cM. While the other linkage map was constructed by F2:9 population, which contained 45 loci in 11 linkage groups, with a full-length coverage of 554.42. Based on the inclusive composite interval mapping method with QTL IciMapping 4.1, 15 QTLs related to upper half mean length, fiber strength, the micronaire value, the elongation and the uniformity were both detected in F2 and F2:3 segregating populations, among them, the QTL locus qFM-4-2 related to the micronaire value explained the highest phenotypic variation rate at 21.10%. QTLs with dominant or super-dominant effects accounted for 66.7% of the total, which showed that dominant genes were the main source of fiber quality heterosis in &lsquo;Ji1518&rsquo;. Meanwhile, 6 QTLs related to the above five traits of fiber quality were detected in the RIL (F2:9) population, and the contribution rate was between 5.10% and 10.26%. QTL loci related with FS and MIC were detected near HAU2349 in all three populations, and QTL loci related with FU were detected near HAU2710 in all three populations, and the markers above were linked on A6 chromosome. These stable and common QTLs are beneficial to the MAS breeding, which could improve the breeding efficiency.

Genetic mapping of morpho-physiological traits involved during reproductive stage drought tolerance in rice.

Reproductive stage drought stress is an important yield reducing factor in rainfed rice. Genetic mapping of morpho-physiological traits under the stress will help to develop cultivars suitable for drought prone environments through marker-assisted breeding (MAB). Though various yield QTLs under reproductive stage drought tolerance are available for MAB, but no robust markers controlling different morho-physiological traits are available for this stress tolerance. QTLs linked to morpho-physiological traits under drought stress were mapped by evaluating 190 F7 recombinant inbred lines (RIL) using bulk segregant analysis (BSA) strategy. Wide variations were observed in the RILs for eleven morpho-physiological traits involved during the stress. A total of 401 SSR primers were surveyed for parental polymorphism of which 77 were detected to be polymorphic. Inclusive composite interval mapping detected a total of five consistent QTLs controlling leaf rolling (qLR9.1), leaf drying (qLD9.1), harvest index (qHI9.1), spikelet fertility (qSF9.1) and relative water content (qRWC9.1) under reproductive stage drought stress. Another two non-allelic QTLs controlling leaf rolling (qLR8.1) and leaf drying (qLD12.1) were also detected to be linked and found to control the two traits. QTL controlling leaf rolling, qLR8.1 was validated in this mapping population and may be useful in MAB programs. Out of these five consistent QTLs, four (qLR9.1, qLD9.1, qHI9.1 and qRWC9.1) were detected to be novel QTLs and useful for MAB for improvement of reproductive stage drought tolerance in rice.

Quantitative trait loci mapping of plant architecture-related traits using the high-throughput genotyping by sequencing method

Plant architecture-related traits are important in breeding maize (Zea mays L.). Suwan maize germplasm has been widely used in tropical/subtropical regions because of its abundant genetic diversity compared to temperate germplasm. To investigate the influence of the genetic base on the detection of quantitative trait loci (QTLs) controlling plant architecture-related traits, a population of 150 F2:3 progeny derived from ZHL908 and HCL645 were developed and genotyped using the genotyping by sequencing (GBS) method. Through inclusive composite interval mapping using 5636 SNP markers, a total of 25 QTL-controlling plant architecture-related traits were identified. Seventeen QTLs had been previously reported, which may be important in future MAS breeding. Eight new QTLs were reported for the first time in this study. Of the 25 QTLs, 7 QTLs were related to plant height (PH), 4 QTLs were related to ear height (EH), 4 QTLs were related to leaf number (LN), 5 QTLs were related to tassel length (TL), and 5 QTLs were related to tassel primary branch number (TPBN). Four plant architectural trait-related genes, sparse inflorescence1, ramosa3, dwarf1, and zea floricaula/leafy1, were found to be located in qLN4, qTL5, qTPBN1 and qTPBN5, respectively. These results not only provide new insights into the genetic research investigating maize plant architecture variation but also provide molecular evidence that may enable the improvement of Suwan germplasm in modern maize breeding.

Construction of a high-density genetic map and QTL mapping of leaf traits and plant growth in an interspecific F1 population of Catalpa bungei \xd7 Catalpa duclouxii Dode

BackgroundCatalpa bungei is an important tree species used for timber in China and widely cultivated for economic and ornamental purposes. A high-density linkage map of C. bungei would be an efficient tool not only for identifying key quantitative trait loci (QTLs) that affect important traits, such as plant growth and leaf traits, but also for other genetic studies.ResultsRestriction site-associated DNA sequencing (RAD-seq) was used to identify molecular markers and construct a genetic map. Approximately 280.77 Gb of clean data were obtained after sequencing, and in total, 25,614,295 single nucleotide polymorphisms (SNPs) and 2,871,647 insertions-deletions (InDels) were initially identified in the genomes of 200 individuals of a C. bungei (7080) × Catalpa duclouxii (16-PJ-3) F1 population and their parents. Finally, 9072 SNP and 521 InDel markers that satisfied the requirements for constructing a genetic map were obtained. The integrated genetic map contained 9593 pleomorphic markers in 20 linkage groups and spanned 3151.63 cM, with an average distance between adjacent markers of 0.32 cM. Twenty QTLs for seven leaf traits and 13 QTLs for plant height at five successive time points were identified using our genetic map by inclusive composite interval mapping (ICIM). Q16–60 was identified as a QTL for five leaf traits, and three significant QTLs (Q9–1, Q18–66 and Q18–73) associated with plant growth were detected at least twice. Genome annotation suggested that a cyclin gene participates in leaf trait development, while the growth of C. bungei may be influenced by CDC48C and genes associated with phytohormone synthesis.ConclusionsThis is the first genetic map constructed in C. bungei and will be a useful tool for further genetic study, molecular marker-assisted breeding and genome assembly.

Detection of quantitative trait loci for salt tolerance in zombi pea [Vigna vexillata (L.) A. Rich

Zombi pea [Vigna vexillata (L.) A. Rich] is an underutilized legume crop, with highly diverse wild species that carry genes conferring resistance to several biotic and abiotic stresses. The objective of this study was to construct a zombi pea genetic linkage map and locate quantitative trait loci related to salt resistance. A zombi pea F2 population (159 individuals) developed from a cross between the salt-resistant wild zombi pea accession JP235908 (var. ovata; female parent) and the salt-susceptible cultivated zombi pea accession TVNu240 (var. macrosperma; male parent) was genotyped with simple sequence repeat (SSR) and restriction site-associated DNA sequencing (RAD-seq) markers. A genetic linkage map with 10 linkage groups (LGs) was constructed based on 379 markers (136 SSR and 243 RAD-seq markers). The map spanned 793.25 cM, with a mean distance between adjacent markers of 2.14 cM. A comparative genome analysis revealed high macro-synteny between zombi pea and mung bean/adzuki bean, although several chromosomal translocations likely occurred in zombi pea. The salt tolerance of the F2:3 population was evaluated at the seedling stage under hydroponic conditions. Inclusive composite interval mapping identified three quantitative trait loci (QTLs) (qSaltol1.1 on LG1, qSaltol2.1 on LG2, and qSaltol6.1 on LG6) related to the salt resistance of the F2 population. The qSaltol1.1, qSaltol2.1, and qSaltol6.1 QTLs explained 13.3%, 7.6%, and 8.1% of the salt-resistance phenotypic variance, respectively. A comparative genome analysis revealed that qSaltol1.1 may correspond to the Saltol1.1 QTL conferring salt tolerance in beach cowpea [Vigna marina (Burm.) Merr.], which is a halophytic species. Moreover, two genes encoding a plasma membrane H+-ATPase and a gene encoding a cation/proton exchanger may contribute to the salt resistance of zombi pea and beach cowpea. These findings may be relevant for the breeding of salt-resistant zombi pea plants.

Characterization of QTLs for Seedling Resistance to Tan Spot and Septoria Nodorum Blotch in the PBW343/Kenya Nyangumi Wheat Recombinant Inbred Lines Population.

Tan spot (TS) and Septoria nodorum blotch (SNB) induced by Pyrenophora tritici-repentis and Parastagonospora nodorum, respectively, cause significant yield losses and adversely affect grain quality. The objectives of this study were to decipher the genetics and map the resistance to TS and SNB in the PBW343/Kenya Nyangumi (KN) population comprising 204 F6 recombinant inbred lines (RILs). Disease screening was performed at the seedling stage under greenhouse conditions. TS was induced by P. tritici-repentis isolate MexPtr1 while SNB by P. nodorum isolate MexSN1. Segregation pattern of the RILs indicated that resistance to TS and SNB in this population was quantitative. Diversity Array Technology (DArTs) and simple sequence repeats (SSRs) markers were used to identify the quantitative trait loci (QTL) for the diseases using inclusive composite interval mapping (ICIM). Seven significant additive QTLs for TS resistance explaining 2.98 to 23.32% of the phenotypic variation were identified on chromosomes 1A, 1B, 5B, 7B and 7D. For SNB, five QTLs were found on chromosomes 1A, 5A, and 5B, explaining 5.24 to 20.87% of the phenotypic variation. The TS QTL on 1B chromosome coincided with the pleiotropic adult plant resistance (APR) gene Lr46/Yr29/Pm39. This is the first report of the APR gene Lr46/Yr29/Pm39 contributing to TS resistance.

QTL mapping for sorghum downy mildew disease resistance in maize (Zea mays L.) in recombinant inbred line population of UMI79 X UMI936 (w)

Sorghum downy mildew (SDM) caused by the Oomycete, Peronosclerospora sorghi ((Weston and Uppal) C. G. Shaw) is a major impediment to maize production and productivity. Identifying genomic regions (QTLs), contributing to SDM resistance will aid in a marker-assisted resistant breeding program. In the present study, QTLs have been mapped for SDM resistance using 158 recombinant inbred lines (RILs) derived from the cross between SDM-susceptible (UMI79) and resistant (UMI936 (w)) inbred lines. Phenotyping for SDM reaction was conducted in three environments under artificial epiphytotic conditions. Inclusive composite interval mapping with simple sequence repeat (SSR) markers resulted in the identification of three putative QTLs, one with major-effect (PVE = 17.1 %) on chromosome three and other two with minor effects on chromosome six (PVE = 2.3) and seven (PVE = 3.4). Inclusive composite interval mapping detected one QTL for the all the three environments, all co-localizing near the same marker, bnlg420 on chromosome 3.