Quantitative Trait Loci For Plant Height Research Articles

Dynamic quantitative trait loci (QTL) for plant height predict biomass yield in hybrid rye (Secale cereale L.)

The biomethane production from agricultural biomass will be a key component of the future energy mix. Rye (Secale cereale L.) is ideally suited for this purpose due to its high adaptability to a wide range of soils, weather and cropping conditions. Its high biomass yield is achieved with the lowest input of fertilizer and pesticides of all small-grain cereals. For the selection of cultivars with high kernel and biomass potential in the same breeding program, a prediction of biomass yield by indirect traits would increase the selection progress. To analyze quantitative-trait loci (QTL) for plant height in three developmental stages (BBCH 32, BBCH 51–55, BBCH 73) and biomass yield, 258 experimental rye hybrids were grown at three and four locations in Germany in 2011 and 2012, respectively. A genetic linkage map was constructed with 911 molecular markers. The QTL analysis identified a total of 18 QTL for plant height at the three assessment dates and of three QTL for dry matter yield at milk ripening. A major QTL on chromosome 2R explained 46, 12, and 25% of the total genetic variance for plant height at BBCH 51–55, BBCH 73, and for biomass yield, respectively. Furthermore, two large-effect QTL for plant height in two growth stages and dry matter yield were identified on chromosomes 3R and 5R. For eleven of the identified QTL in rye the respective QTL/genes on syntenic rice chromosomes were detected that could serve as candidate genes in follow-up experiments. A set of sequence-tagged site (STS) markers flanking the three QTL alleles for dry matter yield (QDmy-2R, QDmy-3R, and QDmy-5R) enables to the achievement of an indirect selection gain for biomass yield. This marker-assisted strategy allows for the screening of large hybrid rye populations already at early developmental stages without the resource-demanding harvest for biomass yield.

Major Co-localized QTL for Plant Height, Branch Initiation Height, Stem Diameter, and Flowering Time in an Alien Introgression Derived Brassica napus DH Population.

Plant height (PH), branch initiation height (BIH), and stem diameter (SD) are three stem-related traits that play crucial roles in plant architecture and lodging resistance. Herein, we show one doubled haploid (DH) population obtained from a cross between Y689 (one Capsella bursa-pastoris derived Brassica napus intertribal introgression) and Westar (B. napus cultivar) that these traits were significantly positively correlated with one another and with flowering time (FT). Based on a high-density SNP map, a total of 102 additive quantitative trait loci (QTL) were identified across six environments. Seventy-two consensus QTL and 49 unique QTL were identified using a two-round strategy of QTL meta-analysis. Notably, a total of 19 major QTL, including 11 novel ones, were detected for these traits, which comprised two QTL clusters on chromosomes A02 and A07. Conditional QTL mapping was performed to preliminarily evaluate the genetic basis (pleiotropy or tight linkage) of the co-localized QTL. In addition, QTL by environment interactions (QEI) mapping was performed to verify the additive QTL and estimate the QEI effect. In the genomic regions of all major QTL, orthologs of the genes involved in phytohormone biosynthesis, phytohormone signaling, flower development, and cell differentiation in Arabidopsis were proposed as candidate genes. Of these, BnaA02g02560, an ortholog of Arabidopsis GASA4, was suggested as a candidate gene for PH, SD, and FT; and BnaA02g08490, an ortholog of Arabidopsis GNL, was associated with PH, BIH and FT. These results provide useful information for further genetic studies on stem-related traits and plant growth adaptation.

The genetic architecture of nodal root number in maize.

The maize nodal root system plays a crucial role in the development of the aboveground plant and determines the yield via the uptake of water and nutrients in the field. However, the genetic architecture of the maize nodal root system is not well understood, and it has become the 'dark matter' of maize genetics. Here, a large teosinte-maize population was analyzed, and high-resolution mapping revealed that 62 out of 133 quantitative trait loci (QTLs), accounting for approximately half of the total genetic variation in nodal root number, were derived from QTLs for flowering time, which was further validated through a transgenic analysis and a genome-wide association study. However, only 16% of the total genetic variation in nodal root number was derived from QTLs for plant height. These results gave a hint that flowering time played a key role in shaping nodal root number via indirect selection during maize domestication. Our results also supported that more aerial nodal roots and fewer crown roots might be favored in temperate maize, and this root architecture might efficiently improve root-lodging resistance and the ability to take up deep water and nitrogen under dense planting.

Rht24 reduces height in the winter wheat population 'Solitär×Bussard' without adverse effects on Fusarium head blight infection.

The dwarfing gene Rht24 on chromosome 6A acts in the wheat population 'Solitär×Bussard', considerably reducing plant height without increasing Fusarium head blight severity and delaying heading stage. The introduction of the Reduced height (Rht)-B1 and Rht-D1 semi-dwarfing genes led to remarkable increases in wheat yields during the Green Revolution. However, their utilization also brings about some unwanted characteristics, including the increased susceptibility to Fusarium head blight. Thus, Rht loci that hold the potential to reduce plant height in wheat without concomitantly increasing Fusarium head blight (FHB) susceptibility are urgently required. The biparental population 'Solitär×Bussard' fixed for the Rht-1 wild-type alleles, but segregating for the recently described gibberellic acid (GA)-sensitive Rht24 gene, was analyzed to identify quantitative trait loci (QTL) for FHB severity, plant height, and heading date and to evaluate the effect of the Rht24 locus on these traits. The most prominent QTL was Rht24 on chromosome 6A explaining 51% of genotypic variation for plant height and exerting an additive effect of -4.80cm. For FHB severity three QTL were detected, whereas five and six QTL were found for plant height and heading date, respectively. No FHB resistance QTL was co-localized with QTL for plant height. Unlike the Rht-1 semi-dwarfing alleles, Rht24b did not significantly affect FHB severity. This demonstrates that the choice of semi-dwarfing genes used in plant breeding programs is of utmost consideration where resistance to FHB is an important breeding target.

Further QTL mapping for yield component traits using introgression lines in rice (Oryza sativa 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 BC3F6,7 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 BC4F2,4 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.

Relationship between QTL for grain shape, grain weight, test weight, milling yield, and plant height in the spring wheat cross RL4452/'AC Domain'.

Kernel morphology characteristics of wheat are complex and quantitatively inherited. A doubled haploid (DH) population of the cross RL4452/‘AC Domain’ was used to study the genetic basis of seed shape. Quantitative trait loci (QTL) analyses were conducted on a total of 18 traits: 14 grain shape traits, flour yield (Fyd), and three agronomic traits (Plant height [Plht], 1000 Grain weight [Gwt], Test weight [Twt]), using data from trial locations at Glenlea, Brandon, and Morden in Manitoba, Canada, between 1999 and 2004. Kernel shape was studied through digital image analysis with an Acurum® grain analyzer. Plht, Gwt, Twt, Fyd, and grain shape QTL were correlated with each other and QTL analysis revealed that QTL for these traits often mapped to the same genetic locations. The most significant QTL for the grain shape traits were located on chromosomes 4B and 4D, each accounting for up to 24.4% and 53.3% of the total phenotypic variation, respectively. In addition, the most significant QTL for Plht, Gwt, and Twt were all detected on chromosome 4D at the Rht-D1 locus. Rht-D1b decreased Plht, Gwt, Twt, and kernel width relative to the Rht-D1a allele. A narrow genetic interval on chromosome 4B contained significant QTL for grain shape, Gwt, and Plht. The ‘AC Domain’ allele reduced Plht, Gwt, kernel length and width traits, but had no detectable effect on Twt. The data indicated that this variation was inconsistent with segregation at Rht-B1. Numerous QTL were identified that control these traits in this population.

Identification of minor effect QTLs for plant architecture related traits using super high density genotyping and large recombinant inbred population in maize (Zea mays)

BackgroundPlant Architecture Related Traits (PATs) are of great importance for maize breeding, and mainly controlled by minor effect quantitative trait loci (QTLs). However, cloning or even fine-mapping of minor effect QTLs is very difficult in maize. Theoretically, large population and high density genetic map can be helpful for increasing QTL mapping resolution and accuracy, but such a possibility have not been actually tested.ResultsHere, we employed a genotyping-by-sequencing (GBS) strategy to construct a linkage map with 16,769 marker bins for 1021 recombinant inbred lines (RILs). Accurately mapping of well studied genes P1, pl1 and r1 underlying silk color demonstrated the map quality. After QTL analysis, a total of 51 loci were mapped for six PATs. Although all of them belong to minor effect alleles, the lengths of the QTL intervals, with a minimum and median of 1.03 and 3.40 Mb respectively, were remarkably reduced as compared with previous reports using smaller size of population or small number of markers. Several genes with known function in maize were shown to be overlapping with or close neighboring to these QTL peaks, including na1, td1, d3 for plant height, ra1 for tassel branch number, and zfl2 for tassel length. To further confirm our mapping results, a plant height QTL, qPH1a, was verified by an introgression lines (ILs).ConclusionsWe demonstrated a method for high resolution mapping of minor effect QTLs in maize, and the resulted comprehensive QTLs for PATs are valuable for maize molecular breeding in the future.

Mating Design and Genetic Structure of a Multi-Parent Advanced Generation Intercross (MAGIC) Population of Sorghum (Sorghum bicolor (L.) Moench).

Multi-parent advanced generation intercross (MAGIC) populations are powerful next-generation mapping resources. We describe here the mating design and structure of the first MAGIC population in sorghum, and test its utility for mapping. The population was developed by intercrossing 19 diverse founder lines through a series of paired crosses with a genetic male sterile (MS) source, followed by 10 generations of random mating. At the final stage of random mating, 1000 random fertile plants in the population were identified and subjected to six generations of selfing to produce 1000 immortal MAGIC inbred lines. The development of this sorghum MAGIC population took over 15 yr. Genotyping-by-sequencing (GBS) of a subset of 200 MAGIC lines identified 79,728 SNPs, spanning high gene-rich regions. Proportion of SNPs per chromosome ranged from 6 to 15%. Structure analyses produced no evidence of population stratification, portraying the desirability of this population for genome-wide association studies (GWAS). The 19 founders formed three clusters, each with considerable genetic diversity. Further analysis showed that 73% of founder alleles segregated in the MAGIC population. Linkage disequilibrium (LD) patterns depicted the MAGIC population to be highly recombined, with LD decaying to r2 0.2 at 40 kb and down to r2 0.1 at 220 kb. GWAS detected two known plant height genes, DWARF1 (chromosome 9) and DWARF3 (chromosome 7), and a potentially new plant height quantitative trait locus (QTL) (QTL-6) on chromosome 6. The MAGIC population was found to be rich in allelic content with high fragmentation of its genome, making it fit for both gene mapping and effective marker-assisted breeding.

Quantitative trait loci associated with short inter-node length in soybean.

Manipulating the genetic control of plant height is essential in soybean breeding to increase yield through the enlargement of the plant size while preventing lodging. A Japanese soybean germplasm, Y2, has distinctively shorter inter-node lengths than those of recently developed Japanese cultivars and is expected to provide new variation to prevent lodging. A quantitative trait loci (QTL) analysis for plant height-related traits was conducted using F2 individuals derived from a cross between the elite Japanese cultivar Fukuyutaka and Y2. A major QTL for average inter-node length (AIL) and plant height was identified on chromosome 13 and named qSI13-1 (QTL for short inter-node on chromosome 13). The Y2 allele of qSI13-1 was partially dominant for plant height. qSI13-1 exhibited no effect on either days to flowering or number of main stem nodes. The AILs and plant heights of the near-isogenic lines containing the Y2 allele of qSI13-1 in the genetic background of Fukuyutaka were significantly less than those of Fukuyutaka. No significant differences between the near-isogenic lines and Fukuyutaka were observed for seed yield and flowering date, indicating that qSI13-1 will be useful in developing cultivars with short plant heights without having negative effects on yield potential and days to flowering.

Mapping QTLs Controlling Flowering Time and Important Agronomic Traits in Pearl Millet.

Pearl millet [Pennisetum glaucum (L.) R. Br.] is a staple crop for the people of arid and semi-arid regions of the world. It is fast gaining importance as a climate resilient nutricereal. Exploiting the bold seeded, semi-dwarf, and early flowering genotypes in pearl millet is a key breeding strategy to enhance yield, adaptability, and for adequate food in resource-poor zones. Genetic variation for agronomic traits of pearl millet inbreds can be used to dissect complex traits through quantitative trait locus (QTL) mapping. This study was undertaken to map a set of agronomically important traits like flowering time (FT), plant height (PH), panicle length (PL), and grain weight (self and open-pollinated seeds) in the recombinant inbred line (RIL) population of ICMB 841-P3 × 863B-P2 cross. Excluding grain weight (open pollinated), heritabilities for FT, PH, PL, grain weight (selfed) were in high to medium range. A total of six QTLs for FT were detected on five chromosomes, 13 QTLs for PH on six chromosomes, 11 QTLs for PL on five chromosomes, and 14 QTLs for 1,000-grain weight (TGW) spanning five chromosomes. One major QTL on LG3 was common for FT and PH. Three major QTLs for PL, one each on LG1, LG2, and LG6B were detected. The large effect QTL for TGW (self) on LG6B had a phenotypic variance (R2) of 62.1%. The R2 for FT, TGW (self), and PL ranged from 22.3 to 59.4%. A total of 21 digenic interactions were discovered for FT (R2 = 18–40%) and PL (R2 = 13–19%). The epistatic effects did not reveal any significant QTL × QTL × environment (QQE) interactions. The mapped QTLs for flowering time and other agronomic traits in present experiment can be used for marker-assisted selection (MAS) and genomic selection (GS) breeding programs.

The Genetic Basis of Plant Architecture in 10 Maize Recombinant Inbred Line Populations.

Plant architecture is a key factor affecting planting density and grain yield in maize (Zea mays). However, the genetic mechanisms underlying plant architecture in diverse genetic backgrounds have not been fully addressed. Here, we performed a large-scale phenotyping of 10 plant architecture-related traits and dissected the genetic loci controlling these traits in 10 recombinant inbred line populations derived from 14 diverse genetic backgrounds. Nearly 800 quantitative trait loci (QTLs) with major and minor effects were identified as contributing to the phenotypic variation of plant architecture-related traits. Ninety-two percent of these QTLs were detected in only one population, confirming the diverse genetic backgrounds of the mapping populations and the prevalence of rare alleles in maize. The numbers and effects of QTLs are positively associated with the phenotypic variation in the population, which, in turn, correlates positively with parental phenotypic and genetic variations. A large proportion (38.5%) of QTLs was associated with at least two traits, suggestive of the frequent occurrence of pleiotropic loci or closely linked loci. Key developmental genes, which previously were shown to affect plant architecture in mutant studies, were found to colocalize with many QTLs. Five QTLs were further validated using the segregating populations developed from residual heterozygous lines present in the recombinant inbred line populations. Additionally, one new plant height QTL, qPH3, has been fine-mapped to a 600-kb genomic region where three candidate genes are located. These results provide insights into the genetic mechanisms controlling plant architecture and will benefit the selection of ideal plant architecture in maize breeding.

Quantitative trait locus mapping under irrigated and drought treatments based on a novel genetic linkage map in mungbean (Vigna radiata L.).

A novel genetic linkage map was constructed using SSR markers and stable QTLs were identified for six drought tolerance related-traits using single-environment analysis under irrigation and drought treatments. Mungbean (Vigna radiata L.) is one of the most important leguminous food crops. However, mungbean production is seriously constrained by drought. Isolation of drought-responsive genetic elements and marker-assisted selection breeding will benefit from the detection of quantitative trait locus (QTLs) for traits related to drought tolerance. In this study, we developed a full-coverage genetic linkage map based on simple sequence repeat (SSR) markers using a recombinant inbred line (RIL) population derived from an intra-specific cross between two drought-resistant varieties. This novel map was anchored with 313 markers. The total map length was 1010.18cM across 11 linkage groups, covering the entire genome of mungbean with a saturation of one marker every 3.23cM. We subsequently detected 58 QTLs for plant height (PH), maximum leaf area (MLA), biomass (BM), relative water content, days to first flowering, and seed yield (Yield) and 5 for the drought tolerance index of 3 traits in irrigated and drought environments at 2 locations. Thirty-eight of these QTLs were consistently detected two or more times at similar linkage positions. Notably, qPH5A and qMLA2A were consistently identified in marker intervals from GMES5773 to MUS128 in LG05 and from Mchr11-34 to the HAAS_VR_1812 region in LG02 in four environments, contributing 6.40-20.06% and 6.97-7.94% of the observed phenotypic variation, respectively. None of these QTLs shared loci with previously identified drought-related loci from mungbean. The results of these analyses might facilitate the isolation of drought-related genes and help to clarify the mechanism of drought tolerance in mungbean.

High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencing

BackgroundGenetic mapping and quantitative trait locus (QTL) detection are powerful methodologies in plant improvement and breeding. White jute (Corchorus capsularis L.) is an important industrial raw material fiber crop because of its elite characteristics. However, construction of a high-density genetic map and identification of QTLs has been limited in white jute due to a lack of sufficient molecular markers. The specific locus amplified fragment sequencing (SLAF-seq) strategy combines locus-specific amplification and high-throughput sequencing to carry out de novo single nuclear polymorphism (SNP) discovery and large-scale genotyping. In this study, SLAF-seq was employed to obtain sufficient markers to construct a high-density genetic map for white jute. Moreover, with the development of abundant markers, genetic dissection of fiber yield traits such as plant height was also possible. Here, we present QTLs associated with plant height that were identified using our newly constructed genetic linkage groups.ResultsAn F8 population consisting of 100 lines was developed. In total, 69,446 high-quality SLAFs were detected of which 5,074 SLAFs were polymorphic; 913 polymorphic markers were used for the construction of a genetic map. The average coverage for each SLAF marker was 43-fold in the parents, and 9.8-fold in each F8 individual. A linkage map was constructed that contained 913 SLAFs on 11 linkage groups (LGs) covering 1621.4 cM with an average density of 1.61 cM per locus. Among the 11 LGs, LG1 was the largest with 210 markers, a length of 406.34 cM, and an average distance of 1.93 cM between adjacent markers. LG11 was the smallest with only 25 markers, a length of 29.66 cM, and an average distance of 1.19 cM between adjacent markers. ‘SNP_only’ markers accounted for 85.54% and were the predominant markers on the map. QTL mapping based on the F8 phenotypes detected 11 plant height QTLs including one major effect QTL across two cultivation locations, with each QTL accounting for 4.14–15.63% of the phenotypic variance.ConclusionsTo our knowledge, the linkage map constructed here is the densest one available to date for white jute. This analysis also identified the first QTL in white jute. The results will provide an important platform for gene/QTL mapping, sequence assembly, genome comparisons, and marker-assisted selection breeding for white jute.

Characterization of the temporal and spatial expression of wheat (Triticum aestivum L.) plant height at the QTL level and their influence on yield-related traits.

The temporal and spatial expression patterns of stable QTL for plant height and their influences on yield were characterized. Plant height (PH) is a complex trait in wheat (Triticum aestivum L.) that includes the spike length (SL) and the internode lengths from the first to the fifth internode, which are counted from the top and abbreviated as FIRITL, SECITL, THIITL, FOUITL, and FIFITL, respectively. This study identified eight putative additive quantitative trait loci (QTL) for PH. In addition, unconditional and conditional QTL mapping were used to analyze the temporal and spatial expression patterns of five stable QTL for PH. qPh-3A mainly regulated SL, FIRITL, and FIFITL to affect PH during the booting-heading stage (BS-HS); qPh-3D regulated all internode lengths to affect PH, especially during the BS-HS; before HS, qPh-4B mainly affected FIRITL, SECITL, THIITL, and FOUITL and qPh-5A.1 mainly affected SECITL, THIITL, and FOUITL to regulate PH; and qPh-6B mainly regulated FIRITL to affect the PH after the booting stage (BS). qPhdv-4B, a QTL for the response of PH to nitrogen stress, was stable and co-localized with qPh-4B. All five stable QTL, except for qPh-3A, were related to the 1000 kernel weight and yield per plant. Regions of qPh-3A, qPh-3D, qPh-4B, qPh-5A.1, and qPh-6B showed synteny to parts of rice chromosomes 1, 1, 3, 9, and 2, respectively. Based on comparative genomics analysis, Rht-B1b was cloned and mapped in the CI of qPh-4B. This report provides useful information for fine mapping of the stable QTL for PH and the genetic improvement of wheat plant type.

A Genome-Wide mQTL-seq Scan Identifies Potential Molecular Signatures Regulating Plant Height in Chickpea

The current study employed a high-throughput genome-wide next-generation sequencing-led multiple QTL-seq (mQTL-seq) strategy in two inter- and intra-specific recombinant inbred line (RIL) mapping populations to identify the major genomic regions underlying robust quantitative trait loci (QTLs) regulating plant height in chickpea. The whole genome resequencing discovered 446,475 and 150,434 high-quality homozygous single nucleotide polymorphisms (SNPs) exhibiting polymorphism between tall and dwarf/semi-dwarf mapping parents and bulk/homozygous individuals selected from each of two chickpea RIL populations. These SNP-led mQTL-seq assays in RIL mapping populations scaled-down two longer major genomic regions (1.26–1.34 Mb) underlying robust plant height QTLs into the shorter high-resolution QTL intervals (653.2–756.3 kb) on chickpea chromosomes 3 and 8. This essentially delineated regulatory novel natural SNP allelic variants from brassinosteroid insensitive 1-receptor kinase 1 (BAK1) and gibberellin (GA) 20-oxidase genes governing plant height in chickpea. A strong impact of evolutionary bottlenecks including strong artificial/natural selection on two plant height gene loci during chickpea domestication was observed. The shoot apical meristem-specific expression aside from down-regulation of two plant height genes especially in dwarf/semi-dwarf as compared to tall parents and homozygous mapping individuals of two aforementioned RIL populations was apparent. The integrated genomics-assisted breeding strategy combining mQTL-seq with differential gene expression profiling and functional allelic diversity-based trait domestication study collectively identified potential natural allelic variants of candidate genes underlying major plant height QTLs in chickpea. These functionally relevant molecular signatures can be of immense use for marker-aided genetic enhancement to develop high seed- and pod-yielding non-lodging cultivars restructured with desirable plant height in chickpea.

QTLs for heading date and plant height under multiple environments in rice.

Both heading date and plant height are important traits related to grain yield in rice. In this study, a recombinant inbred lines (RILs) population was used to map quantitative trait loci (QTLs) for both traits under 3 long-day (LD) environments and 1 short-day (SD) environment. A total of eight QTLs for heading date and three QTLs for plant height were detected by composite interval mapping under LD conditions. Additional one QTL for heading date and three QTLs for plant height were identified by Two-QTL model under LD conditions. Among them, major QTLs qHd7.1, qHd7.2 and qHd8 for heading date, and qPh1 and qPh7.1 for plant height were commonly detected. qHd7.1 and qHd7.2 were mapped to small regions of less than 1cM. Genome position comparison of previously cloned genes with QTLs detected in this study revealed that qHd5 and qPh3.1 were two novel QTLs. The alleles of these QTLs increasing trait values were dispersed in both parents, which well explained the transgressive segregation observed in this population. In addition, the interaction between qHd7.1 and qHd8 was detected under all LD conditions. Multiple-QTL model analysis revealed that all QTLs and their interactions explained over 80% of heading date variation and 50% of plant height variation. Two heading date QTLs were detected under SD condition. Of them, qHd10 were commonly identified under LD condition. The difference in QTL detection between LD and SD conditions indicated most heading date QTLs are sensitive to photoperiod. These findings will benefit breeding design for heading date and plant height in rice.

Both major and minor QTL associated with plant height can be identified using near-isogenic lines in maize

Plant height (PH) and ear height (EH) are important agronomic traits in maize (Zea mays L.) breeding. To investigate the influence of the genetic background on the detection of quantitative trait locus (QTL) conferring PH and EH, related mapping populations were developed from a near isogenic line (NIL) and its recurrent parent. Through joint-environment analyses, a total of four QTLs for PH were identified within the introgressed regions of the used NIL. Compared with the mapping results of RILs, extra PH QTLs could be detected within the target region of the used NIL on chromosome 4, but a previous PH QTL within this region was lost. The missed detection of a previous PH QTL also occurred on chromosome 6. As such, the genetic background of the recurrent parent exerted its influence on the detection of height QTL in this study. Meanwhile, according to the analyses of recombination events, qPEH6, a major height QTL on chromosome 6, was narrowed down to a region of approximately 1 Mb. Sequence analysis revealed that GRMZM2G014119, which encodes an ubiquitin-like protein related to the auxin response, was roughly assumed to be the candidate gene responsible for qPEH6.

Development and deployment of a high-density linkage map identified quantitative trait loci for plant height in peanut (Arachis hypogaea L.).

Plant height is one of the most important architecture traits in crop plants. In peanut, the genetic basis of plant height remains ambiguous. In this context, we genotyped a recombinant inbred line (RIL) population with 140 individuals developed from a cross between two peanut varieties varying in plant height, Zhonghua 10 and ICG 12625. Genotyping data was generated for 1,175 SSR and 42 transposon polymorphic markers and a high-density genetic linkage map was constructed with 1,219 mapped loci covering total map length of 2,038.75 cM i.e., accounted for nearly 80% of the peanut genome. Quantitative trait locus (QTL) analysis using genotyping and phenotyping data for three environments identified 8 negative-effect QTLs and 10 positive-effect QTLs for plant height. Among these QTLs, 8 QTLs had a large contribution to plant height that explained ≥10% phenotypic variation. Two major-effect consensus QTLs namely cqPHA4a and cqPHA4b were identified with stable performance across three environments. Further, the allelic recombination of detected QTLs proved the existence of the phenomenon of transgressive segregation for plant height in the RIL population. Therefore, this study not only successfully reported a high-density genetic linkage map of peanut and identified genomic region controlling plant height but also opens opportunities for further gene discovery and molecular breeding for plant height in peanut.

Development and Evaluation of Chromosome Segment Substitution Lines Carrying Overlapping Chromosome Segments of the Whole Wild Rice Genome.

Common wild rice (Oryza rufipogon Griff.) represents an important resource for rice improvement. Genetic populations provide the basis for a wide range of genetic and genomic studies. In particular, chromosome segment substitution lines (CSSLs) are most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs). In this study, 146 CSSLs were produced; they were derived from the crossing and back-crossing of two rice cultivars: Dongnanihui 810 (Oryza sativa L.), an indica rice cultivar as the recipient, and ZhangPu wild rice, a wild rice cultivar as the donor. First, a physical map of the 146 CSSLs was constructed using 149 molecular markers. Based on this map, the total size of the 147 substituted segments in the population was 1145.65 Mb, or 3.04 times that of the rice genome. To further facilitate gene mapping, heterozygous chromosome segment substitution lines (HCSSLs) were also produced, which were heterozygous in the target regions. Second, a physical map of the 244 HCSSLs was produced using 149 molecular markers. Based on this map, the total length of substituted segments in the HCSSLs was 1683.75 Mb, or 4.47 times the total length of the rice genome. Third, using the 146 CSSLs, two QTLs for plant height, and one major QTL for apiculus coloration were identified. Using the two populations of HCSSLs, the qPa-6-2 gene was precisely mapped to an 88 kb region. These CSSLs and HCSSLs may, therefore, provide powerful tools for future whole genome large-scale gene discovery in wild rice, providing a foundation enabling the development of new rice varieties. This research will also facilitate fine mapping and cloning of quantitative trait genes, providing for the development of superior rice varieties.

Quantitative Trait Loci (QTL) Identification in the Progeny of a Polycross

Connected multiparental crosses are valuable for detecting quantitative trait loci (QTL) with multiple alleles. The objective of this study was to show that the progeny of a polycross can be considered as connected mutiparental crosses and used for QTL identification. This is particularly relevant in outbreeding species showing strong inbreeding depression and for which synthetic varieties are created. A total of 191 genotypes from a polycross with six parents were phenotyped for plant height (PH) and plant growth rate (PGR) and genotyped with 82 codominant markers. Markers allowed the identification of the male parent for each sibling and so the 191 genotypes were divided into 15 full-sib families. The number of genotypes per full-sib family varied from 2 to 28. A consensus map of 491 cM was built and QTL were detected with MCQTL-software dedicated to QTL detection in connected mapping populations. Two major QTL for PH and PGR in spring were identified on linkage groups 3 and 4. These explained from 12% to 22% of phenotypic variance. The additive effects reached 12.4 mm for PH and 0.11 mm/C°d for PGR. This study shows that the progenies of polycrosses can be used to detect QTL.