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2022 ◽  
Vol 12 ◽  
Author(s):  
Yijing Gao ◽  
Shan Zhou ◽  
Yuxin Huang ◽  
Baoqing Zhang ◽  
Yuhui Xu ◽  
...  

Sugarcane is one of the most important industrial crops globally. It is the second largest source of bioethanol, and a major crop for biomass-derived electricity and sugar worldwide. Smut, caused by Sporisorium scitamineum, is a major sugarcane disease in many countries, and is managed by smut-resistant varieties. In China, smut remains the single largest constraint for sugarcane production, and consequently it impacts the value of sugarcane as an energy feedstock. Quantitative trait loci (QTLs) associated with smut resistance and linked diagnostic markers are valuable tools for smut resistance breeding. Here, we developed an F1 population (192 progeny) by crossing two sugarcane varieties with contrasting smut resistance and used for genome-wide single nucleotide polymorphism (SNP) discovery and mapping, using a high-throughput genotyping method called “specific locus amplified fragment sequencing (SLAF-seq) and bulked-segregant RNA sequencing (BSR-seq). SLAF-seq generated 148,500 polymorphic SNP markers. Using SNP and previously identified SSR markers, an integrated genetic map with an average 1.96 cM marker interval was produced. With this genetic map and smut resistance scores of the F1 individuals from four crop years, 21 major QTLs were mapped, with a phenotypic variance explanation (PVE) > 8.0%. Among them, 10 QTLs were stable (repeatable) with PVEs ranging from 8.0 to 81.7%. Further, four QTLs were detected based on BSR-seq analysis. aligning major QTLs with the genome of a sugarcane progenitor Saccharum spontaneum, six markers were found co-localized. Markers located in QTLs and functional annotation of BSR-seq-derived unigenes helped identify four disease resistance candidate genes located in major QTLs. 77 SNPs from major QTLs were then converted to Kompetitive Allele-Specific PCR (KASP) markers, of which five were highly significantly linked to smut resistance. The co-localized QTLs, candidate resistance genes, and KASP markers identified in this study provide practically useful tools for marker-assisted sugarcane smut resistance breeding.


2021 ◽  
Author(s):  
Frank Dunemann ◽  
Wanying He ◽  
Christoph Böttcher ◽  
Sven Reichardt ◽  
Thomas Nothnagel ◽  
...  

Abstract Background Falcarinol-type polyacetylenes (PAs) such as falcarinol (FaOH) and falcarindiol (FaDOH) are produced by several Apiaceae vegetables such as carrot, parsnip, celeriac and parsley. They are known for numerous biological functions and contribute to the undesirable bitter off-taste of carrots and their products. Despite their interesting biological functions, the genetic basis of their structural diversity and function is widely unknown. A better understanding of the genetics of the PA levels present in carrot roots might support breeding of carrot cultivars with tailored PA levels for food production or nutraceuticals. Results A large carrot F2 progeny derived from a cross of a cultivated inbred line with an inbred line derived from a Daucus carota ssp. commutatus accession rich in PAs was used for linkage mapping and quantitative trait locus (QTL) analysis. Ten QTLs for FaOH and FaDOH levels in roots were identified in the carrot genome. Major QTLs for FaOH and FaDOH with high LOD values of up to 40 were identified on chromosomes 4 and 9. To discover putative candidate genes from the plant fatty acid metabolism, we examined an extended version of the inventory of the carrot FATTY ACID DESATURASE2 (FAD2) gene family. Additionally, we used the carrot genome sequence for a first inventory of ECERIFERUM1 (CER1) genes possibly involved in PA biosynthesis. We identified genomic regions on different carrot chromosomes around the found QTLs, that contain several FAD2 and CER1 genes within their 2-LOD confidence intervals. With regard to the major QTLs on chromosome 9 three putative CER1 decarbonylase gene models are proposed as candidate genes. Conclusion The present study increases the current knowledge on the genetics of PA accumulation in carrot roots. Our finding, that carrot candidate genes from the fatty acid metabolism are significantly associated with major QTLs for both major PAs, will facilitate future functional gene studies and a further dissection of the genetic factors controlling PA accumulation. Characterization of such candidate genes will have a positive impact on carrot breeding programs aimed at both lowering or increasing PA concentrations in carrot roots.


Author(s):  
Ravi Koppolu ◽  
Guojing Jiang ◽  
Sara G. Milner ◽  
Quddoos H. Muqaddasi ◽  
Twan Rutten ◽  
...  

Abstract Key message Spikelet indeterminacy and supernumerary spikelet phenotypes in barley multiflorus2.b mutant show polygenic inheritance. Genetic analysis of multiflorus2.b revealed major QTLs for spikelet determinacy and supernumerary spikelet phenotypes on 2H and 6H chromosomes. Abstract Understanding the genetic basis of yield forming factors in small grain cereals is of extreme importance, especially in the wake of stagnation of further yield gains in these crops. One such yield forming factor in these cereals is the number of grain-bearing florets produced per spikelet. Wild-type barley (Hordeum vulgare L.) spikelets are determinate structures, and the spikelet axis (rachilla) degenerates after producing single floret. In contrast, the rachilla of wheat (Triticum ssp.) spikelets, which are indeterminate, elongates to produce up to 12 florets. In our study, we characterized the barley spikelet determinacy mutant multiflorus2.b (mul2.b) that produced up to three fertile florets on elongated rachillae of lateral spikelets. Apart from the lateral spikelet indeterminacy (LS-IN), we also characterized the supernumerary spikelet phenotype in the central spikelets (CS-SS) of mul2.b. Through our phenotypic and genetic analyses, we identified two major QTLs on chromosomes 2H and 6H, and two minor QTLs on 3H for the LS-IN phenotype. For, the CS-SS phenotype, we identified one major QTL on 6H, and a minor QTL on 5H chromosomes. Notably, the 6H QTLs for CS-SS and LS-IN phenotypes co-located with each other, potentially indicating that a single genetic factor might regulate both phenotypes. Thus, our in-depth phenotyping combined with genetic analyses revealed the quantitative nature of the LS-IN and CS-SS phenotypes in mul2.b, paving the way for cloning the genes underlying these QTLs in the future.


2021 ◽  
Author(s):  
Liu Jin ◽  
Xiaoding Ma ◽  
Huiying Zhou ◽  
Shuhui Li ◽  
Di Cui ◽  
...  

Abstract Climate change has a negative effect on rice production and food security. High temperature stress is a major obstacle and can significantly reduce yield. A set of recombinant inbred lines (RILs) derived from the cross between Longdao5 (heat-sensitive) and Zhongyouzao8 (heat-tolerant) was used in the identification of heat tolerant QTL. Spikelet fertility (SF) and heat tolerance (HT) indexes showed a significant difference among the parents and RILs population, and SF and HT have different of effect under natural and artificial high temperature conditions. Sixty-one QTLs were detected on chromosomes 1-8, 10 and 12, while 25, 27 and 14 additive QTLs were identified under the control, natural and artificial high temperature conditions, respectively. Pleiotropic effects and QTL hotspots are the key factors affecting these traits, three key major QTL clusters qHTSF1, qHTSF4, and qHTSF12 can be stably expressed. In addition, epistatic effect is an important component in the regulation of heat tolerance. A total of 17 pairs of epistatic interaction loci were detected, and these additive QTL clusters have a significant epistatic effect. Bulk segregant analysis (BSA) method was proved to be a convenient method to detect major QTLs. Three QTLs, namely qSF1, qSF2 and qSF12 were detected under high temperature environment, and there is a highly significant correlation among these addictive QTLs. These results will lay the foundation for the further fine mapping of these major QTLs and enrich the molecular marker-assisted selection of heat-tolerant gene resources in rice breeding.


2021 ◽  
Author(s):  
Tao Li ◽  
Qiao Li ◽  
Jinhui Wang ◽  
Zhao Yang ◽  
Yanyan Tang ◽  
...  

Abstract Background: Yield-related traits including thousand grain weight (TGW), grain number per spike (GNS), grain width (GW), grain length (GL), plant height (PH), spike length (SL), and spikelet number per spike (SNS) are greatly associated with wheat (Triticum aestivum L.) grain yield. To detect quantitative trait loci (QTL) associated with them, 193 recombinant inbred lines derived from two elite winter wheat varieties Chuanmai42 and Chuanmai39 were employed to perform QTL mapping in six or eight environments. Results: A total of 30 QTLs on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 4A, 5A, 5B, 6A, 6D, 7A, 7B and 7D were identified. Among them, six major QTLs QTgw.cib-6A.1, QTgw.cib-6A.2, QGw.cib-6A, QGl.cib-3A, QGl.cib-6A, and QSl.cib-2D explaining 5.96-23.75% of the phenotypic variance were detected in multiple environments and showed strong and stable effects on corresponding traits. Three QTL clusters on chromosomes 2D and 6A containing 10 QTLs were also detected, which showed significant pleiotropic effects on multiple traits. Additionally, three Kompetitive Allele Specific PCR (KASP) markers linked to five of these major QTLs were developed. Candidate genes of QTgw.cib-6A.1/QGl.cib-6A and QGl.cib-3A were analyzed based on the spatiotemporal expression patterns, gene annotation, and orthologous search. Conclusions: Six major QTLs for TGW, GL, GW and SL were detected. Three KASP markers linked with five of these major QTLs were developed. These QTLs and KASP markers will be useful for elucidating the genetic architecture of grian yield and developing new wheat varieties with high and stable yield in wheat.


2021 ◽  
Vol 12 ◽  
Author(s):  
Uday Chand Jha ◽  
Harsh Nayyar ◽  
Ramesh Palakurthi ◽  
Rintu Jha ◽  
Vinod Valluri ◽  
...  

In the context of climate change, heat stress during the reproductive stages of chickpea (Cicer arietinum L.) leads to significant yield losses. In order to identify the genomic regions responsible for heat stress tolerance, a recombinant inbred line population derived from DCP 92-3 (heat sensitive) and ICCV 92944 (heat tolerant) was genotyped using the genotyping-by-sequencing approach and evaluated for two consecutive years (2017 and 2018) under normal and late sown or heat stress environments. A high-density genetic map comprising 788 single-nucleotide polymorphism markers spanning 1,125 cM was constructed. Using composite interval mapping, a total of 77 QTLs (37 major and 40 minor) were identified for 12 of 13 traits. A genomic region on CaLG07 harbors quantitative trait loci (QTLs) explaining >30% phenotypic variation for days to pod initiation, 100 seed weight, and for nitrogen balance index explaining >10% PVE. In addition, we also reported for the first time major QTLs for proxy traits (physiological traits such as chlorophyll content, nitrogen balance index, normalized difference vegetative index, and cell membrane stability). Furthermore, 32 candidate genes in the QTL regions that encode the heat shock protein genes, heat shock transcription factors, are involved in flowering time regulation as well as pollen-specific genes. The major QTLs reported in this study, after validation, may be useful in molecular breeding for developing heat-tolerant superior lines or varieties.


PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0254526
Author(s):  
Ravindra Ramrao Kale ◽  
Ch. V. Durga Rani ◽  
M. Anila ◽  
H. K. Mahadeva Swamy ◽  
V. P. Bhadana ◽  
...  

With an objective of mapping novel low soil P (Phosphorus) tolerance loci in the non-Pup1 type donor rice line, Wazuhophek, we screened a recombinant inbred line (RIL) mapping population consisting of 330 lines derived from the cross Wazuhophek x Improved Samba Mahsuri (which is highly sensitive to low soil P) in a plot with low soil P for tolerance associated traits. Molecular mapping with SSR markers revealed a total of 16 QTLs (seven major and nine minor QTLs), which are associated with low soil P tolerance related traits. Interestingly, a QTL hotspot, harbouring 10 out of 16 QTLs were identified on the short arm of chromosome 8 (flanked by the makers RM22554 and RM80005). Five major QTLs explaining phenotypic variance to an extent of 15.28%, 17.25%, 21.84%, 20.23%, and 18.50%, associated with the traits, plant height, shoot length, the number of productive tillers, panicle length and yield, respectively, were located in the hotspot. Two major QTLs located on chromosome 1, associated with the traits, total biomass and root to shoot ratio, explaining 15.44% and 15.44% phenotypic variance, respectively were also identified. Complex epistatic interactions were observed among the traits, grain yield per plant, days to 50% flowering, dry shoot weight, and P content of the seed. In-silico analysis of genomic regions flanking the major QTLs revealed the presence of key putative candidate genes, possibly associated with tolerance.


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