scholarly journals Identification, pyramid and candidate genes of QTLs for associated traits based on a dense erect panicle rice CSSL-Z749 and five SSSLs, three DSSLs and one TSSL

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Dachuan Wang ◽  
Kai Zhou ◽  
Siqian Xiang ◽  
Qiuli Zhang ◽  
Ruxiang Li ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Candidate Genes ◽  
Complex Traits ◽  
Seed Set ◽  
Average Length ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Minor Qtls ◽  
Segment Substitution ◽  
Major Qtl

Abstract Background Seed-set density is an important agronomic trait in rice. However, its genetic mechanism is complex. Chromosome segment substitution lines (CSSLs) are ideal materials for studying complex traits. Results A rice CSSL, Z749, with a dense and erect panicle phenotype, was identified among progeny of the recipient parent Nipponbare and the donor parent Xihui 18. Z749 carried seven substitution segments (average length 2.12 Mb). Compared with Nipponbare, Z749 showed significant increases in the numbers of primary (NPB) and secondary branches (NSB), number of spikelets (SPP) and grains per panicle (GPP), seed-set density (SSD), and decrease in panicle length (PL). A secondary F2 population derived from a cross between Nipponbare and Z749 was used to map quantitative trait loci (QTLs) for associated traits. Fifteen QTLs distributed on chromosomes 5, 7, 8, and 10 were detected. The QTL qPL7 might be an allele of OsFAD8 and the remaining 14 QTLs (e.g., qSSD5 and qSSD10 etc.) might be novel. Fourteen QTLs were verified using five single-segment substitution lines (SSSLs). The seed-set density of Z749 was controlled predominantly by one major QTL (qSSD10) and two minor QTLs (qSSD5 and qSSD8). The QTLs qSSD10, qSSD5, and qSSD8 were fine-mapped to intervals of 1.05, 1.46, and 1.53 Mb on chromosomes 10, 5, and 8, respectively. Analysis of QTL additive effects indicated that qSSD5, qSSD8, and qSSD10 from Xihui18 increased seed-set density of Z749 by 14.10, 11.38, and 5.11 spikelets per 10 cm panicle, respectively. Analysis of QTL epistatic effects revealed that pyramiding of qSSD5 and qSSD8, qSSD5 and qSSD10, qSSD8 and qSSD10, and qSSD5, qSSD8 and qSSD10 produced novel genotypes with increased seed-set density. Conclusions Inheritance of seed-set density in Z749 was controlled predominantly by one major QTL (qSSD10) and two minor QTLs (qSSD5 and qSSD8). Then, they were fine-mapped to intervals of 1.05, 1.46, and 1.53 Mb on chromosomes 10, 5, 8, respectively. Two MAPK genes (OsMPK9 and OsMPK17) and one gene (candidate gene 6) involved in auxin metabolism might be candidate genes for qSSD5, and OsSAUR32 might be the candidate gene for qSSD8. Pyramiding of qSSD5, qSSD8, and qSSD10 enhanced seed-set density.

scholarly journals Identification, Pyramid and Candidate Genes of QTLs for Associated Traits Based on a Dense Erect Panicle Rice CSSL-Z749 and Five SSSLs, Three DSSLs and One TSSL

2021 ◽  
Author(s):  
Dachuan Wang ◽  
Kai Zhou ◽  
Siqian Xiang ◽  
Qiuli Zhang ◽  
Ruxiang Li ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Candidate Genes ◽  
Complex Traits ◽  
Seed Set ◽  
Average Length ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Minor Qtls ◽  
Segment Substitution ◽  
Major Qtl

Abstract Background Seed-set density is an important agronomic trait in rice. However, its genetic mechanism is complex. Chromosome segment substitution lines (CSSLs) are ideal materials for studying complex traits. Results A rice CSSL, Z749, with a dense and erect panicle phenotype, was identified among progeny of the recipient parent Nipponbare and the donor parent Xihui 18. Z749 carried seven substitution segments (average length 2.16 Mb). Compared with Nipponbare, Z749 showed significant increases in the numbers of primary (NPB) and secondary branches (NSB), number of spikelets (SPP) and grains per panicle (GPP), seed-set density (SSD), and decrease in panicle length (PL). A secondary F2 population derived from a cross between Nipponbare and Z749 was used to map quantitative trait loci (QTLs) for associated traits. Fifteen QTLs distributed on chromosomes 5, 7, 8, and 10 were detected. The QTL qPL7 might be an allele of OsFAD8 and the remaining 14 QTLs (e.g., qSSD5 and qSSD10 etc.) might be novel. Fourteen QTLs were verified using five single-segment substitution lines (SSSLs). The seed-set density of Z749 was controlled predominantly by one major QTL (qSSD10) and two minor QTLs (qSSD5 and qSSD8). The QTLs qSSD10, qSSD5, and qSSD8 were fine-mapped to intervals of 1.05, 1.46, and 1.53 Mb on chromosomes 10, 5, and 8, respectively. Analysis of QTL additive effects indicated that qSSD5, qSSD8, and qSSD10 from Xihui18 increased seed-set density of Z749 by 14.1, 11.38, and 5.11 spikelets per 10 cm panicle, respectively. Analysis of QTL epistatic effects revealed that pyramiding of qSSD5 and qSSD8, qSSD5 and qSSD10, qSSD8 and qSSD10, and qSSD5, qSSD8 and qSSD10 produced novel genotypes with increased seed-set density. Conclusions Inheritance of seed-set density in Z749 was controlled predominantly by one major QTL (qSSD10) and two minor QTLs (qSSD5 and qSSD8). Then, they were fine-mapped to intervals of 1.05, 1.46, and 1.53 Mb on chromosomes 10, 5, 8, respectively. Two MAPK genes (OsMPK9 and OsMPK17) and one gene (candidate gene 6) involved in auxin metabolism might be candidate genes for qSSD5, and OsSAUR32 might be the candidate gene for qSSD8. Pyramiding of qSSD5, qSSD8, and qSSD10 enhanced seed-set density.

scholarly journals Identification and Pyramid of QTLs Based on Rice Short-wide Grain CSSL-Z414, SSSL, DSSL and Candidate Gene Analysis of qGL11 and qGW5

2021 ◽  
Author(s):  
Juan Li ◽  
Hongxia Yang ◽  
Guangyi Xu ◽  
Keli Deng ◽  
Jinjin Yu ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Complex Traits ◽  
Average Length ◽  
Brown Rice ◽  
Pcr Analysis ◽  
Substitution Lines ◽  
Grain Length ◽  
Qrt Pcr ◽  
Grain Width ◽  
Segment Substitution

Abstract BackgroundMost of rice agronomic traits as grain length etc. are complex traits controlled by multiple genes. Chromosome segment substitution lines (CSSLs) are ideal materials for dissecting and studying of these complex traits. ResultsA rice short-wide grain CSSL Z414 was identified among progeny of the recipient parent Xihui 18 (an indica restorer line) and the donor parent Huhan 3 (a japonica cultivar). Z414 carried 4 substitution segments (average length was 3.04 Mb), and displayed shorter panicle length and less number of primary branches, shorter, wider and larger grain, higher brown rice rate and chalkiness degree when compared with Xihui 18. Then, 9 quantitative trait loci (QTLs) for associated traits were identified using the secondary F2 population from Xihui 18 / Z414. Among them, 6 QTLs (qPL3, qGW5, qGL11, qRLW5, qRLW11, qGWT5) could be verified by corresponding single segment substitution lines (SSSLs, S1-S6). In addition, 4 QTLs (qGL3, qGL5, qCD3 and qCD5) were detected by S1 and S5, which was not detected by the F2 population. Thus, the grain length of Z414 was controlled by qGL11, qGL3 and qGL5, and the grain width of Z414 was answered by qGW5. Then by substitution mapping, qGL11 and qGW5 were delimited within the estimated substitution length of 1.42 and 1.14 Mb on chromosomes 11 and 5, and 4 and 2 candidate genes were found respectively for qGL11 and qGW5 by sequencing. However, only two had expression differences by qRT-PCR analysis. Finally, Analysis of QTL epistatic effects revealed that pyramid of qGL3 (a= 0.22) and qGL11 (a=-0.19) caused grain length of double segment substitution line (DSSL, D2) shorter than that of S5 (qGL11).ConclusionsWe developed a rice short –wide grain CSSL with 4 substitution segments from Huhan 3 based on the genetic backgrounds of Xihui 18. The grain width of Z414 was controlled by qGW5, and GS5 should be the candidate gene for qGW5 by sequencing and qRT-PCR analysis. The grain length of Z414 was controlled by qGL11, qGL3, and qGL5, and CycT1;3 should be the best candidate gene of qGL11, whose specific function of regulating grain length was still unknown, and qGL11 is epistatic to qGL3.

Identification, Pyramid and Candidate gene of QTL for Yield-related Traits Based on Rice CSSLs in Indica Xihui18 Background

2021 ◽  
Author(s):  
Shuangfei Sun ◽  
Siqian Xiang ◽  
Meng Lv ◽  
Kai Zhou ◽  
Juan Li ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Candidate Genes ◽  
Target Genes ◽  
Molecular Design ◽  
Mechanism Analysis ◽  
Substitution Lines ◽  
Cell Width ◽  
Analysis And Design ◽  
Single Segment Substitution Lines ◽  
Segment Substitution

Abstract Chromosome segment substitution line (CSSL) in rice is important for functional analysis and design breeding of target genes. Here, a novel rice CSSL-Z431 was identified from indica restorer line Xihui18 as recipient and Huhan3 as donor. Z431 contained six segments from Huhan3, with an average substitution length of 2.12 Mb. Compared with Xihui18, Z431 increased panicles per plant (PN) and displayed short-wide grains. The short-wide grain of Z431 were caused by reducing of cell length and increasing of cell width in the glume. Then, thirteen QTLs were identified in a secondary F2 population derived from Xihui18/Z431. Among them, six QTLs (qPN3, qGL3, qGW5, qRLW2, qRLW3, qGWT-5-2) were validated by four single-segment substitution lines (SSSLs, S1-S4) developed in F3. In addition, thirteen QTLs (qPN1, qPN2, qPL1, qPL2, qGPP1, qGPP2, qGL2, qGW1, qGW2, qGW3, qRLW5-2, qRLW1, qGWT2) were detected by these SSSLs, while not be identified in the F2 population from Xihui18/Z431. Increase of panicles per plant in Z431 was controlled by qPN3, qPN1 and qPN2. OsIAGLU should be the candidate gene for qPN3 by DNA sequencing. The short-wide grain of Z431 was controlled by qGL3, qGL2, qGW5, qGW2 and qGW3. By sequencing between Xihui18 and according SSSL, three candidate genes for qGL3 and two candidate genes for qGW5 were identified, respectively. In addition, pyramid of different QTLs (qPN1and qPN3; qPN2 and qPN3 etc.) yielded different epistatic effects. These results lay good foundation in molecular mechanism analysis of unreported genes and rice molecular design breeding.

Identification of QTLs Associated with Two-seed Pod Length and Width in Soybean

2021 ◽  
Author(s):  
D.P. Shan ◽  
J.G. Xie ◽  
Y. Yu ◽  
R. Zhou ◽  
Z.L. Cui ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Gene Annotation ◽  
Soybean Seed ◽  
Chromosome 17 ◽  
Substitution Lines ◽  
Epistatic Effects ◽  
Chromosome Segment Substitution Lines ◽  
Trait Locus ◽  
Segment Substitution ◽  
Pod Length

Background: Two-seed pod length and width (TSPL and TSPW, respectively) are the traits underlying seed size, which is an important factor influencing soybean yield. Methods: A population comprising 213 chromosome segment substitution lines from a cross between ‘Suinong14’ (SN14) and ZYD00006 was used for a quantitative trait locus (QTL) analysis. The QTLs were identified on the basis of the phenotypes from 2016 to 2019. Additionally, IciMapping 4.2 was used to analyze the phenotypic and genetic data. Genes were annotated using the KEGG and Phytozome databases. Result: Five QTLs for TSPL and four QTLs for TSPW were identified. One QTL on chromosome 17 was detected for TSPL in 2017 and 2018 as well for TSPW in 2018 and 2019. Analyses of the additive × additive epistatic effects of QTLs revealed six stable loci pairs for epistatic effects on the two traits. On the basis of an alignment of the parental gene sequences and the gene annotation information, Glyma.04G188800, Glyma.11G164700, Glyma.13G132700, Glyma.17G156100 and Glyma.13G133200 were selected as candidate genes for TSPL, whereas Glyma.13G174400, Glyma.13G174700, Glyma.16G012500, Glyma.17G156100, Glyma.19G161700 and Glyma.19G161800 were selected as candidate genes for TSPW. These results may be relevant for future attempts to modify soybean seed traits.

scholarly journals Whole-Genome Sequencing of 117 Chromosome Segment Substitution Lines for Genetic Analyses of Complex Traits in Rice

Rice ◽  
2022 ◽  
Vol 15 (1) ◽  
Author(s):  
Jiongjiong Fan ◽  
Hua Hua ◽  
Zhaowei Luo ◽  
Qi Zhang ◽  
Mengjiao Chen ◽  
...  
Keyword(s):  
Complex Traits ◽  
Molecular Breeding ◽  
Agronomic Traits ◽  
Chromosome Segment ◽  
Segment Length ◽  
Whole Genome ◽  
Substitution Lines ◽  
Genetic Analyses ◽  
Chromosome Segment Substitution Lines ◽  
Segment Substitution

AbstractRice is one of the most important food crops in Asia. Genetic analyses of complex traits and molecular breeding studies in rice greatly rely on the construction of various genetic populations. Chromosome segment substitution lines (CSSLs) serve as a powerful genetic population for quantitative trait locus (QTL) mapping in rice. Moreover, CSSLs containing target genomic regions can be used as improved varieties in rice breeding. In this study, we developed a set of CSSLs consisting of 117 lines derived from the recipient ‘Huanghuazhan’ (HHZ) and the donor ‘Basmati Surkb 89–15’ (BAS). The 117 lines were extensively genotyped by whole-genome resequencing, and a high-density genotype map was constructed for the CSSL population. The 117 CSSLs covered 99.78% of the BAS genome. Each line contained a single segment, and the average segment length was 6.02 Mb. Using the CSSL population, we investigated three agronomic traits in Shanghai and Hangzhou, China, and a total of 25 QTLs were detected in both environments. Among those QTLs, we found that RFT1 was the causal gene for heading date variance between HHZ and BAS. RFT1 from BAS was found to contain a loss-of-function allele based on yeast two-hybrid assay, and its causal variation was a P to S change in the 94th amino acid of the RFT1 protein. The combination of high-throughput genotyping and marker-assisted selection (MAS) is a highly efficient way to construct CSSLs in rice, and extensively genotyped CSSLs will be a powerful tool for the genetic mapping of agronomic traits and molecular breeding for target QTLs/genes.

scholarly journals Discovery and Fine Mapping of qSCR6.01, a Novel Major QTL Conferring Southern Rust Resistance in Maize

Plant Disease ◽  
2020 ◽  
Vol 104 (7) ◽  
pp. 1918-1924
Author(s):  
Lu Lu ◽  
Zhennan Xu ◽  
Suli Sun ◽  
Qing Du ◽  
Zhendong Zhu ◽  
...  
Keyword(s):  
Phenotypic Variation ◽  
Recombinant Inbred Lines ◽  
Recurrent Parent ◽  
Chromosome 6 ◽  
Substitution Lines ◽  
Resistance Qtl ◽  
Chromosome Segment Substitution Lines ◽  
Total Phenotypic Variation ◽  
Segment Substitution ◽  
Major Qtl

Southern corn rust (SCR), an airborne disease caused by Puccinia polysora, can severely reduce the yield of maize (Zea mays L.). Using recombinant inbred lines (RILs) derived from a cross between susceptible inbred line Ye478 and resistant Qi319 in combination with their high-density genetic map, we located five quantitative trait loci (QTLs) against SCR, designated as qSCR3.04, qSCR5.07, qSCR6.01, qSCR9.03, and qSCR10.01, on chromosomes 3, 5, 6, 9, and 10, respectively. Each QTL could explain 2.84 to 24.15% of the total phenotypic variation. qSCR6.01, detected on chromosome 6, with the highest effect value, accounting for 17.99, 23.47, and 24.15% of total phenotypic variation in two environments and best linear unbiased prediction, was a stably major resistance QTL. The common confidence interval for qSCR6.01 was 2.95 Mb based on the B73 RefGen_v3 sequence. The chromosome segment substitution lines (CSSLs) constructed with Qi319 as the donor parent and Ye478 as the recurrent parent were used to further verify qSCR6.01 resistance to SCR. The line CL183 harboring introgressed qSCR6.01 showed obvious resistance to SCR that was distinctly different from that of Ye478 (P = 0.0038). Further mapping of qSCR6.01 revealed that the resistance QTL was linked to insertion-deletion markers Y6q77 and Y6q79, with physical locations of 77.6 and 79.6 Mb, respectively, on chromosome 6. Different from previous major genes or QTLs against SCR on chromosome 10, qSCR6.01 was a newly identified major QTL resistance to SCR on chromosome 6 for the first time. Using RIL and CSSL populations in combination, the SCR-resistance QTL research can be dissected effectively, which provided important gene resource and genetic information for breeding resistant varieties.

scholarly journals Fine Mapping of A QTL Locus (QNFSP07-1) And Analysis of Candidate Genes For Four-Seeded Pods In Soybean

2021 ◽  
Author(s):  
Yingying Li ◽  
Chunyan Liu ◽  
Nannan Wang ◽  
Zhanguo Zhang ◽  
Lilong Hou ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Candidate Genes ◽  
Developmental Stages ◽  
Gene Annotation ◽  
High Ratio ◽  
Recurrent Parent ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Gene Map ◽  
Segment Substitution

Abstract The number of four-seeded pods is a quantitative trait in soybean [Glycine max (L.) Merr.] and is closely related to yield in terms of breeding. In this study, individuals with high ratio of four-seed pods which from chromosome segment substitution lines (CSSLs) that can be stably inherited were selected as the parent, and Suinong 14 (SN14) was used as recurrent parent to construct secondary mapping population via marker-assisted selection. The initial QTL mapping interval was 0.67 Mb and was located on Gm07. Based on the initial QTL mapping results, individuals that were heterozygous at the interval (36116118-37399738 bp) were screened, and the heterozygous individuals were subjected to inbreeding to obtain 13 F3 populations, with a target interval of 321 kb. Gene annotation was performed on the finely mapped interval, and 27 genes were obtained. Glyma.07G200900, Glyma.07G201200 were identified as candidate genes. qRT-PCR was used to measure the expression of the candidate genes at different developmental stages of soybean. The expression levels of the 2 candidate genes in terms of cell division (axillary buds, COTs, EMs) were higher than those in terms of cell expansion (MM, LM), and these genes play a positive regulatory role in the formation of four-seeded pods. Haplotype analysis shows that Glyma.07G201200 has two excellent haplotypes. Those results provide the information for gene map-based cloning and molecular marker assisted breeding of the number of four-seeded pod in soybean.

scholarly journals Fine Mapping of a Novel Major Quantitative Trait Locus, qPAA7, That Controls Panicle Apical Abortion in Rice

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaolei Wang ◽  
Lingfeng Li ◽  
Xiaotang Sun ◽  
Jie Xu ◽  
Linjuan Ouyang ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Gene Annotation ◽  
Functional Characterization ◽  
Recurrent Parent ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Trait Locus ◽  
Segment Substitution

The panicle apical abortion (PAA) causes severe yield losses in rice production, but details about its development and molecular basis remain elusive. Here, we detected PAA quantitative trait loci (QTLs) in three environments using a set of chromosome segment substitution lines (CSSLs) that was constructed with indica Changhui121 as the recurrent parent and japonica Koshihikari as the donor parent. First, we identified a novel major effector quantitative trait locus, qPAA7, and selected a severe PAA line, CSSL176, which had the highest PAA rate among CSSLs having Koshihikari segments at this locus. Next, an F2 population was constructed from a cross between CSS176 and CH121. Using F2 to make recombinantion analysis, qPAA7 was mapped to an 73.8-kb interval in chromosome 7. Among nine candidate genes within this interval, there isn’t any known genes affecting PAA. According to the gene annotation, gene expression profile and alignment of genomic DNA, LOC_Os07g41220 and LOC_Os07g41280 were predicted as putative candidate genes of qPAA7. Our study provides a foundation for cloning and functional characterization of the target gene from this locus.

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