Bayesian QTL mapping for recombinant inbred lines derived from a four-way cross

Recombinant inbred lines (RILs) are created by a cross between inbred lines followed by repeated selfing or sib-mating, which include many different types of new inbred lines with many recombination events on the genome. The phenotype of each RIL can be assessed based on multiple individuals within the same line to reduce non-genetic variability. Therefore, RILs are useful tools for QTL mapping allowing effective detection and fine localization of QTL. Usually only two inbred lines are involved to create RILs. In such two-way RILs, however, there are at most two different alleles at QTL and only QTL segregating between two parental lines can be detected. Recently a new crossing design using multiple founders for creating RILs was proposed in Arabidopsis thaliana and mice, where the genome of each RIL is a mosaic of the genomes from multiple parents. Such multi-way RILs are more useful to improve the efficiency in QTL detection than two-way RILs because of the increased chance of QTL segregation among multiple lines, leading to the successful detection of many QTL. In this paper, we propose a Bayesian method for mapping multiple QTL simultaneously in four-way RILs allowing the inference about the equivalence relationship among the four possible alleles descended from the four founder lines as well as the estimation of QTL locations and effects via a MCMC algorithm. Simulation experiments show that our method has the practical ability to detect QTL and to provide the information of equivalence relationship among alleles at detected QTL using four-way RILs.     

大麦重组自交系群体籽粒总花色苷含量和千粒重QTL定位

以云南特有的紫色大麦紫光芒裸二棱和澳大利亚引进的黄色大麦Schooner构建的193个重组自交系为材料,对2013—2015年3年3个试验点的大麦籽粒总花色苷含量和千粒重进行相关性分析和QTL定位。大麦总花色苷含量和千粒重之间呈显著或极显著负相关。共检测到12个总花色苷含量QTL,分别位于1H、2H、4H、6H和7H染色体,贡献率为5.06%～23.86%; 8个千粒重QTL,分别位于2H、4H和7H染色体,贡献率为4.67%～42.32%。贡献率大于10%的QTL有10个,大于20%的有5个,最大的可达42.32%。其中至少2年2点重复检测到2个总花色苷含量QTL,分别位于2H Bmag0125–GBM1309和7H EBmatc0016–Bmag0206区间,可分别解释表型变异的13.66%～17.76%和13.07%～16.43%;3年3点重复检测到2个千粒重QTL,分别位于2HScssr03381–scssr07759和7H GBM1297-GBM1303区间,可分别解释表型变异的4.67%～14.55%和34.51%～42.32%,其加性作用方向均一致。控制总花色苷含量与千粒...     

Identification of QTL for stalk sugar-related traits in a population of recombinant inbred lines of maize

Increasing sugar content in silage maize stalk improves its forage quality and palatability. The genetic mapping and characterization of quantitative trait loci (QTLs) is considered a valuable tool for trait enhancement, yet little information on QTL for stalk sugar content in maize has been reported. To this end, we investigated QTLs associated with stalk sugar traits including Brix, plant height (PHT), three ear leaves area (TELA), and days to silking (DTS) in two environments using a population of 202 recombinant inbred lines from a cross between YXD053, which has a high stalk sugar content, and Y6-1, which has a low stalk sugar content. A genetic map with 180 SSR and 10 AFLP markers was constructed, which spanned 1,648.6 cM of the maize genome with an average marker distance of 8.68 cM, and QTLs were detected using composite interval mapping. Seven QTLs controlling Brix were mapped on chromosomes 1, 2, 6 and 9 in the combined environments. These QTLs could explain 2.69–13.08 % of the phenotypic variance. One major QTL for Brix on chromosome 2 located between the markers bnlg1909 and umc1635 explained 13.08 % of the phenotypic variance. Y6-1 also contributed QTL allele for increased Brix on chromosome 6. One major QTLs controlling PHT on chromosome 1 and TELA on chromosome 4 were also identified and accounted for 13.68 and 12.49 % of the phenotypic variance, respectively. QTL alleles for increased DTS were located on chromosomes 1 and 5 of YXD053. Significant epistatic effects were identified in four traits, but no significant QTL × environment interactions were observed. The information presented here may be valuable for stalk sugar content improvement via marker-assisted selection in silage maize breeding programs.     

Comparative genome mapping of Sorghum bicolor (L.) Moench using an RFLP map constructed in a population of recombinant inbred lines

A restriction fragment length polymorphism (RFLP) linkage map of Sorghum bicolor (L.) Moench was constructed in a population of 137 F_6-8 recombinant inbred lines using sorghum, maize, oat, barley and rice DNA clones. The map consists of 10 linkage groups (LGs) and 323 markers, 247 of which (76.5%) were ordered at a LOD score ≥ 3.0. The LGs comprise from 61 (LG A) to 13 markers (J), which range in length from 205 (A) to 55 cM (J) and have a combined total length of 1347 cM. Highly significant distorted segregation was detected at all of the 38 loci in a 103-cM segment of LG A, the allelic ratios in the segment ranging from approximately 3:1 (one end) to 19:1 (middle) to 2:1 (other end). Duplicated loci located in different LGs have been mapped with 55 of the 295 DNA probes used in the study (18.6%). The distribution of these loci does not provide support for the hypothesis that Sorghum bicolor (L.) Moench is of tetraploid origin. Comparison of the map with RFLP maps of maize, rice, and oat produced evidence for sorghum-maize LG rearrangements and homoeologies not reported previously, including evidence that: (1) a segment of maize 5L and a segment of 5S may be homoeologous to sorghum LGA; (2) maize LGs 4 and 6 are partly homoeologous to sorghum LGE; (3) the short arm of maize LG 2 is partly homoeologous to sorghum LGF; (4) maize LG 4 may be partly homoeologous to sorghum LG G; (5) maize LG 5 and sorghum LG G contain a larger amount of homoeologous genetic material than previously indicated; and (6) a short segment of maize LG 1 may be homoeologous to a short segment of sorghum LG I.     

Genetic mapping and QTL analysis of fruit and flower related traits in cucumber (Cucumis sativus L.) using recombinant inbred lines

A set of 224 recombinant inbred lines (RILs) derived from a narrow cross between two fresh eaten types (S94 (Northern China type) × S06 (Northern European type)) (Cucumis sativus L.) was used to construct a genetic linkage map. With the RILs a 257-point genetic map was constructed including 206 SRAPs, 22 SSRs, 25 SCARs, 1 STS, and three economically important morphological markers (small spines (ss), uniform immature fruit color (u), dull fruit skin (D)). The seven linkage groups covered 1005.9 cM with a mean marker interval of 3.9 cM. The ss locus was linked to D and u, and they were all on Linkage group 6. The RIL map contained a total of 51 sequence-specific markers, which made possible the comparison of molecular linkage maps developed in different laboratories. Using the F_6:7 derived families, a total of 78 QTLs were detected with relatively high LOD scores (2.9–84.4) for nine fruit-related traits (fruit weight, length, and diameter, fruit flesh thickness, seed-cavity diameter, fruit-stalk length, fruit pedicel length, length/diameter and length/stalk ratio) and three flower-related traits (first flower node, first female flower node and female flower ratios). Several sequence-anchor markers (CSWCT25, CS30, CMBR41, CS08 etc.) were closely linked with some QTLs for fruit weight, fruit length, fruit flesh thickness and sex expression, which can be used for the future marker-assisted selection to improve the fruit traits in cucumber breeding. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. X. J. Yuan and J. S. Pan contributed equally to this investigation.     

Genetic analysis and QTL mapping of oil content and seed index using two recombinant inbred lines and two backcross populations in Upland cotton

Cottonseed is one of the main by‐products of cotton. To explore the genetic composition of oil content (OC) and seed index (SI) is helpful for utilizing the cottonseed. Under multiple environmental conditions, the genetic structures of OC and SI were explored using two recombinant inbred lines (RILs) and corresponding backcross (BC) populations in Upland cotton. Twenty‐four and 31 quantitative trait loci (QTLs) for OC and SI, respectively, were detected using composite interval mapping, in which 9 QTLs for OC and 18 QTLs controlling SI were simultaneously identified in more than two environments or two populations. Forty‐seven and 37 QTLs with main effects (M‐QTLs) for OC and SI and 114 and 74 QTLs involved in digenic interactions (E‐QTLs), respectively, identified by inclusive composite interval mapping. On average, the E‐QTLs explained a larger portion of the phenotypic variation than the M‐QTLs did. It was concluded that additive effects of single‐locus and epistasis derived from complementary loci with few detectable single‐locus effects played an important role in oil content and seed index in Upland cotton.     

Quantitative trait loci for grain-quality traits across a rice F2 population and backcross inbred lines

Improving grain-quality is an important goal in rice breeding programs. One vital step is to find major quantitative trait loci (QTLs) for quality related traits and then investigate the relationships among them. We crossed ‘N22’, an indica variety with good appearance but low grain weight, to a japonica variety, ‘Nanjing35’, with superior grain yield but poor appearance. This enabled us to construct an F₂ population and a set of backcross inbred lines (BILs) for QTL-mapping for the traits related grain appearance. In all, 37 QTLs were identified for grain length (GL), grain width (GW), grain thickness (GT), thousand-grain weight (TGW), and the percentage of grains with chalkiness (PGWC). Of these, 17 QTLs detected from 184 plants in the F₂ population explained 4.97–27.26 % of the phenotypic variance, another 20 QTLs were identified using BILs from 2009 to 2010. Quantitative trait loci for major effects were detected in different populations and across years. A new QTL hot spot (marker interval RM504–RM520) was found on Chromosome 3, which harbored QTLs for GL, GW, GT, and TGW. Among our five examined traits, grain shape was significantly correlated with TGW and PGWC. The PGWC values of two heavier grains BILs, L93, and L145 are much lower than Nanjiing35, the analysis of genotype showed that this greater weight may due to the locus for GL occurring within RM504–RM520 on Chromosome 3. Therefore, those two lines will allow us to develop a long-grain high-yield rice variety with less chalkiness.     

A SNP genetic linkage map based on the ‘Hamilton’ by ‘Spencer’ recombinant inbred line population identified QTL for seed isoflavone contents in soybean

Soybean is one of the most important crops worldwide for its protein and oil as well as the health beneficial phytoestrogens or isoflavone. This study reports a relatively dense single nucleotide polymorphism (SNP)‐based genetic map based on ‘Hamilton’ by ‘Spencer’ recombinant inbred line population and quantitative trait loci (QTL) for seed isoflavone contents. The genetic map is composed of 1502 SNP markers and covers about 1423.72 cM of the soybean genome. Two QTL for seed isoflavone contents have been identified in this population. One major QTL that controlled both daidzein (qDZ1) and total isoflavone contents (qTI1) was found on LG C2 (Chr 6). And a second QTL for glycitein content (qGT1) was identified on the LG G (Chr 18). These two QTL in addition to others identified in soybean could be used in soybean breeding to optimize isoflavone content. This newly assembled soybean linkage map is a useful tool to identify and map QTL for important agronomic traits and enhance the identification of the genes involved in these traits.     

Use of recombinant substitution lines for gene mapping and QTL analysis of bread making quality in wheat

Three populations of 41 to 74 homozygous recombinant substitutionlines (RSLs) were used for RFLP mapping and quantitative trait analysis ofthe following parameters: total proteins (%prot), SDS-sedimentationvolume (SDSsed), bread mixing time (Bmxt) and loaf volume (Blvol). TheRSLs were developed from crosses between disomic substitution linesinvolving chromosomes 1A, 1B, and 1D of the high-quality wheat cv.`Cheyenne' (Cnn) substituted into the genetic background of the poorquality cv. `Chinese Spring' (CS). The QTL analysis indicated regions in thethree chromosomes responsible for the differences between CS and thethree disomic substitution lines. The major effect detected on chromosome1A of Cnn was high SDSsed, Bmxt and Blvol associated with the H-M-WGlutenin subunit locus Glu-A1. In addition a QTL was identifieddistally on the long arm of chromosome 1A for Bmxt and Blvol. Ahigh %prot QTL was mapped on the long arm of chromosome 1B of CSand a high Bmxt QTL was mapped on the long arm of chromosome 1B ofCnn. Additionally, this chromosome enhanced SDSsed, Bmxt and Blvol,which were associated with the region of the gliadin and L-M-W Gluteninsubunit locus Gli-B1/Glu-B3. A second more proximal region on theshort arm of chromosome 1B could be involved in loaf volume. QTLanalyses for% prot, showed a strong clear QTL mapped in the centromericregion (XTri/Centromere linkage group) of chromosome 1D with anapparent positive effect brought by CS. For Blvol we revealed two QTLs inopposite phase: one in the Xtri/Centromere region with a positive effect ofCS allele, one in the Glu-D1 region with a positive effect of Cnnallele. This organization `in repulsion' in the parental lines could explain thesmall difference between them for Blvol and the significant transgressionobserved among the RSLs. No clear candidate gene explained the positiveeffect of the centromeric region of CS on %prot and Blvol. Contrary to thecurrent belief that wheat bread-making quality is determined primarily byvariation at the Glu-1 locus, present results showed that the trait isunder a complex control and the Glu-1 loci was only a component ofthe genetic control of the trait.     

Quantitative analysis and QTL mapping for agronomic and fiber traits in an RI population of upland cotton

Genetic mapping is an essential tool for cotton (Gossypium hirsutum L.) molecular breeding and application of DNA markers for cotton improvement. In this present study, we evaluated an RI population including 188 RI lines developed from 94 F₂-derived families and their two parental lines, ‘HS 46’ and ‘MARCABUCAG8US-1-88’, at Mississippi State, MS, for two years. Fourteen agronomic and fiber traits were measured. One hundred forty one (141) polymorphic SSR markers were screened for this population and 125 markers were used to construct a linkage map. Twenty six linkage groups were constructed, covering 125 SSR loci and 965 cM of overall map distance. Twenty four linkage groups (115 SSR loci) were assigned to specific chromosomes. Quantitative genetic analysis showed that the genotypic effects accounted for more than 20% of the phenotypic variation for all traits except fiber perimeter (18%). Fifty six QTLs (LOD > 3.0) associated with 14 agronomic and fiber traits were located on 17 chromosomes. One QTL associated with fiber elongation was located on linkage group LGU01. Nine chromosomes in sub-A genome harbored 27 QTLs with 10 associated with agronomic traits and 17 with fiber traits. Eight chromosomes in D sub-genome harbored 29 QTLs with 13 associated with agronomic traits and 16 with fiber traits. Chromosomes 3, 5, 12, 13, 14, 16, 20, and 26 harbor important QTLs for both yield and fiber quality compared to other chromosomes. Since this RI population was developed from an intraspecific cross within upland cotton, these QTLs should be useful for marker assisted selection for improving breeding efficiency in cotton line development. Paper number J1116 of the Mississippi Agricultural and Forestry Experiment Station, Mississippi State University, Mississippi State, MS 39762. Mention of trademark, proprietary product, or vendor does not constitute a guarantee or warranty of the product by USDA, ARS and does not imply its approval to the exclusion of other products or vendors that may also be suitable.     

QTL analysis for wheat falling number in a recombinant inbred line population segregated with 1BL/1RS translocation in a rainfed agricultural area of China

Falling number (FN) is an inner quality trait in wheat (Triticum aestivum L.) ultimately determining the end use of wheat kernels. In this 3-year study, 171 recombinant inbred lines derived from Chuannong17 (a 1BL/1RS tranlocation parent) × Mianyang11 were planted in the Sichuan Basin, a rainfed agricultural area in southwestern China. In this climate, we found that FN had significant differences between 1BL/1RS translocation lines and non-1BL/1RS translocation lines in two of the 3 years and the heavy fluctuation of rainfall and temperature resulted in decreasing FN in grain filling period. We used 191 simple sequence repeats markers to construct a genetic linkage map and then detected 11 additive effect FN quantitative trait loci (QTL) on chromosomes 2B, 3D, 4A, 4D, 6B and 7D, explaining 5.48–31.91% of the phenotypic variance. The FN QTL on chromosomes 4A, 4D and 6B were major or stable and detected at least in 2 years, whereas the Qfn.sicau-3D.1 in 2015 year explained the maximum phenotypic variation (about 31.91%). Furthermore, FN QTLs additive and epistatic effects as well as their interactions with environment were estimated by a mixed linear model approach. We found that the additive effect QTLs had no significant additive × environment interaction, while the paired QTLs had significant additive × additive epistatic effects however none had a significant additive × additive epistasis × environment interaction effect, excluding the paired QTLs Qfn.sicau-3B/Qfn.sicau-5B.     

Capturing genetic variability and selection of traits for heat tolerance in a chickpea recombinant inbred line (RIL) population under field conditions

Chickpea is the most important pulse crop globally after dry beans. Climate change and increased cropping intensity are forcing chickpea cultivation to relatively higher temperature environments. To assess the genetic variability and identify heat responsive traits, a set of 296 F_8–9 recombinant inbred lines (RILs) of the cross ICC 4567 (heat sensitive) × ICC 15614 (heat tolerant) was evaluated under field conditions at ICRISAT, Patancheru, India. The experiment was conducted in an alpha lattice design with three replications during the summer seasons of 2013 and 2014 (heat stress environments, average temperature 35 °C and above), and post-rainy season of 2013 (non-stress environment, max. temperature below 30 °C). A two-fold variation for number of filled pods (FPod), total number of seeds (TS), harvest index (HI), percent pod setting (%PodSet) and grain yield (GY) was observed in the RILs under stress environments compared to non-stress environment. A yield penalty ranging from 22.26% (summer 2013) to 33.30% (summer 2014) was recorded in stress environments. Seed mass measured as 100-seed weight (HSW) was the least affected (6 and 7% reduction) trait, while %PodSet was the most affected (45.86 and 44.31% reduction) trait by high temperatures. Mixed model analysis of variance revealed a high genotypic coefficient of variation (GCV) (23.29–30.22%), phenotypic coefficient of variation (PCV) (25.69–32.44%) along with high heritability (80.89–86.89%) for FPod, TS, %PodSet and GY across the heat stress environments. Correlation studies (r = 0.61–0.97) and principal component analysis (PCA) revealed a strong positive association among the traits GY, FPod, VS and %PodSet under stress environments. Path analysis results showed that TS was the major direct and FPod was the major indirect contributors to GY under heat stress environments. Therefore, the traits that are good indicators of high grain yield under heat stress can be used in indirect selection for developing heat tolerant chickpea cultivars. Moreover, the presence of large genetic variation for heat tolerance in the population may provide an opportunity to use the RILs in future-heat tolerance breeding programme in chickpea.     

QTL analysis for cooking traits of super rice with a high‐density SNP genetic map and fine mapping of a novel boiled grain length locus

Hybrid rice has contributed substantially to the improvement of grain production worldwide, yet its poor cooking and tasting characteristics have long been recognized. In this study, 132 recombinant inbred lines derived from LYPJ were used to identify quantitative trait loci (QTLs) for 12 cooking traits with the high‐density SNP linkage map recently developed by our team. We identified 17 QTLs on chromosomes 1, 2, 4, 5, 6, 7, 8, 9 and 11, which accounted for 7.50% to 23.50% of the phenotypic variations. A novel major QTL qBGL7 for boiled grain length was further fine‐mapped to an interval of 440 Kb between the two markers RM21906 and gl3 using a BC₃F₂ population. Two near‐isogenic lines with extreme boiled grain length, GX5‐176 and GX5‐101, could be directly used in improving cooking quality. We also identified a QTL for soaked grain width expansion rate, qSGWE6, in the Wx gene region on chromosome 6. The Wx differential regulation coincided with sequential variation between the two parents. Our work offered a theoretical basis for molecular breeding of high‐quality hybrid rice.     

QTL mapping for chromium-induced growth and zinc, and chromium distribution in seedlings of a rice DH population

Chromium contamination in soil has become a severe threat to crop production and food safety. The experiment was conducted using a rice DH population to detect the QTLs associated with Cr tolerance. Seventeen putative QTLs associated with growth traits included three additive loci and fourteen epistatic loci. These loci were distributed on 11 rice chromosomes, and their contribution to the phenotypic variation ranged from 2.44 to 10.08%. Two QTLs located at the similar genetic region on chromosome ten were associated with shoot Cr concentration and translocation from roots to shoots, respectively; and they accounted for 11.65 and 11.22% of the phenotypic variation. In addition, six QTLs related to Zn concentration and translocation was found on chromosomes 1, 2, 4, 5, 7 and 12. Meanwhile epistatic effect existed in the two additive QTLs of qRZC1 and qRZC7. Most of QTLs controlling Zn concentration had small genotypic variance and qSRZ4 related to Zn translocation showed growth condition-dependent expression.     

Quantitative trait locus mapping for seed artificial aging traits using an F2:3 population and a recombinant inbred line population crossed from two highly related maize inbreds

Quantitative trait locus (QTL) mapping for seed longevity is essential for breeding modern cultivars with resistance to deterioration during postharvest storage. The inbred lines X178 and I178 showed large differences in seed vigour after artificial aging treatment, while they had similar performances in terms of most agronomic traits. An F_2:3 population and a recombinant inbred line (RIL) population were generated to map QTL after 5 days under artificial aging conditions. Positive correlations were observed among all investigated traits including the aging germination rate, relative aging germination rate, aging simple vigour index, aging primary root length, aging shoot length and aging total length. Thirteen QTL were identified to locate on five chromosome regions: Chr.1:297 Mb (chromosome 1 region 297 Mb), Chr.3:205 Mb, Chr.4:240 Mb, Chr.5:205 Mb and Chr.7:155 Mb, with 2 to 4 QTL co‐located on a region. In each region, 3–8 previously identified aging‐related QTL were located, confirming the importance of these regions for controlling seed longevity in different maize populations. Taken together, the results of this work provide a foundation for further QTL fine mapping and the molecular‐assisted breeding of aging tolerant maize.     

QTL mapping for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum × Gossypium barbadense

A high-density molecular marker linkage map of cotton based entirely on polymerase chain reaction-based markers is useful for a marker-assisted breeding program. Four kinds of markers—simple sequence repeats (SSRs), sequence-related amplified polymorphism (SRAP), random amplified polymorphic DNA (RAPD), and retrotransposon-microsatellite amplified polymorphism (REMAP)—were used to assay an F₂ population from a cross between “Handan208” (Gossypium hirsutum) and “Pima90” (Gossypium barbadense). Sixty-nine F₂ plants were used for map construction using 834 SSRs, 437 SRAPs, 107 RAPDs, and 16 REMAPs. Linkage analysis revealed that 1,029 loci could be mapped to 26 linkage groups that extended for 5,472.3 cM, with an average distance between 2 loci of 5.32 cM. The corresponding 69 F_2:3 families were grown, arranged in two replicates, and scored for eight phenotypes. Quantitative trait loci (QTL) analysis was performed by means of composite interval mapping using WinQtlCart ver 2.0. A total of 52 distinct QTLs were detected: 4 QTLs for lint index, 8 for seed index, 11 for lint yield, 4 for seed cotton yield, 9 for number of seed per boll, 3 for fiber strength, 5 for fiber length, and 8 for micronaire value. The present map and QTL analysis may provide a useful tool for breeders to transfer desirable traits from G. barbadense to the mainly cultivated species, G. hirsutum.