Rapid Excavating a FLOWERING LOCUS T-Regulator NF-YA Using Genotyping-by-Sequencing

Abstract Soybean [Glycine max (L.) Merrill] is one of the most important crop plants in the world as an important source of protein for both human consumption and livestock fodder. Soybean flowering time is beneficial to the improvement of soybean yield. Therefore, finding new QTLs and further identifying candidate genes associated with various flowering time are fundamental approaches in enhancing the yield of soybean. In this study, a set of 120 recombinant inbred lines (RILs) which developed from a cross of two soybean cultivars, Suinong4 (SN4) and ZK168, were genotyped by genotyping-by-sequencing (GBS) approach and phenotyped to expand the cognitive of flowering time (R1) by Quantitative Trait Loci (QTL) analysis. Eventually, we detected three stable QTLs related to R1 separately located on chromosome 14, 18, and 19 under long-day conditions. The candidate genes of the three QTLs were predicted, and association analysis of the candidate genes related to flowering time was carried out. Moreover, a transient transfection assay was performed and showed that a candidate gene of the QTL on chromosome 19, GmNF-YA21 (Nuclear factor YA21), might affect flowering by suppressing the expression of GmFTs. QTLs detected in this study will provide fundamental resources for finding candidate genes and clarify the mechanisms of flowering which would be helpful for breeding novel high-yield soybean cultivars.

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QTL Analysis of Stem Elongation and Flowering Time in Lettuce Using Genotyping-by-Sequencing

Genes ◽

10.3390/genes12060947 ◽

2021 ◽

Vol 12 (6) ◽

pp. 947

Author(s):

O New Lee ◽

Keita Fukushima ◽

Han Yong Park ◽

Saneyuki Kawabata

Keyword(s):

Flowering Time ◽

Candidate Genes ◽

Genomic Sequence ◽

Stem Elongation ◽

Recombinant Inbred Lines ◽

Genotyping By Sequencing ◽

Stem Growth ◽

Number Of Leaves ◽

Leaf Lettuce ◽

Mapping Populations

Lettuce plants tend to undergo floral initiation by elongation of flower stalks (bolting) under high-temperature and long-day conditions, which is a serious problem for summer lettuce production. Our objective was to generate a high-density genetic map using SNPs obtained from genotyping-by-sequencing (GBS) analysis of F5 recombinant inbred lines (RILs) and to map QTLs involved in stem growth and flowering time in lettuce. A set of 127 intra-specific RIL mapping populations derived from a cross between two varieties, green and red leaf lettuce, were used to identify QTLs related to the number of days from sowing to bolting (DTB), to flowering of the first flower (DTF), to seed-setting of the first flower (DTS), and the total number of leaves (LN), plant height (PH), and total number of branches of main inflorescence (BN) for two consecutive years. Of the 15 QTLs detected, one that controls DTB, DTF, DTS, LN, and PH detected on LG 7, and another QTL that controls DTF, DTS, and PH detected on LG 1. Analysis of the genomic sequence corresponding to the QTL detected on LG 7 led to the identification of 22 putative candidate genes. A consistent QTL related to bolting and flowering time, and corresponding candidate genes has been reported. This study will be valuable in revealing the genetic basis of stem growth and flowering time in lettuce.

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Genome-wide association study reveals candidate genes for flowering time in cowpea (Vigna unguiculata [L.] Walp)

10.1101/2021.04.01.438123 ◽

2021 ◽

Author(s):

Dev Paudel ◽

Rocheteau Dareus ◽

Julia Rosenwald ◽

Maria Munoz-Amatriain ◽

Esteban Rios

Keyword(s):

Flowering Time ◽

Candidate Genes ◽

Vigna Unguiculata ◽

Association Studies ◽

Snp Markers ◽

Genome Wide Association ◽

Human Consumption ◽

Phenotypic Variance ◽

Genome Wide Association Studies ◽

Genome Wide

Cowpea (Vigna unguiculata [L.] Walp., diploid, 2n = 22) is a major crop used as a protein source for human consumption as well as a quality feed for livestock. It is drought and heat tolerant and has been bred to develop varieties that are resilient to changing climates. Plant adaptation to new climates and their yield are strongly affected by flowering time. Therefore, understanding the genetic basis of flowering time is critical to advance cowpea breeding. The aim of this study was to perform genome-wide association studies (GWAS) to identify marker trait associations for flowering time in cowpea using single nucleotide polymorphism (SNP) markers. A total of 367 accessions from a cowpea mini-core collection were evaluated in Ft. Collins, CO in 2019 and 2020, and 292 accessions were evaluated in Citra, FL in 2018. These accessions were genotyped using the Cowpea iSelect Consortium Array that contained 51,128 SNPs. GWAS revealed seven reliable SNPs for flowering time that explained 8-12% of the phenotypic variance. Candidate genes including FT, GI, CRY2, LSH3, UGT87A2, LIF2, and HTA9 that are associated with flowering time were identified for the significant SNP markers. Further efforts to validate these loci will help to understand their role in flowering time in cowpea, and it could facilitate the transfer of some of this knowledge to other closely related legume species.

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Genotyping by sequencing of 393 Sorghum bicolor BTx623 × IS3620C recombinant inbred lines improves sensitivity and resolution of QTL detection

10.1101/308478 ◽

2018 ◽

Author(s):

WenQian Kong ◽

Changsoo Kim ◽

Dong Zhang ◽

Hui Guo ◽

Xu Tan ◽

...

Keyword(s):

Flowering Time ◽

Plant Height ◽

Recombinant Inbred ◽

Recombinant Inbred Lines ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Ril Population ◽

Trait Locus ◽

Number Of Individuals ◽

Syntenic Regions

AbstractWe describe a genetic map with a total of 381 bins of 616 genotyping by sequencing (GBS)-based SNP markers in a F6-F8 recombinant inbred line (RIL) population of 393 individuals derived from crossing S. bicolor BTx623 to S. bicolor IS3620C, a guinea line substantially diverged from BTx623. Five segregation distorted regions were found with four showing enrichment for S. bicolor alleles, suggesting possible selection during formation of this RIL population. A quantitative trait locus (QTL) study with this number of individuals, tripled relative to prior studies of this cross, provided resources, validated previous findings, and demonstrated improved power to detect plant height and flowering time related QTLs relative to other published studies. An unexpected low correlation between flowering time and plant height permitted us to separate QTLs for each trait and provide evidence against pleiotropy. Ten non-random syntenic regions conferring QTLs for the same trait suggest that those QTLs may represent alleles at genes functioning in the same manner since the 96 million year ago genome duplication that created these syntenic relationships, while syntenic regions conferring QTLs for different trait may suggest sub-functionalization after duplication. Collectively, this study provides resources for marker-assisted breeding, as well as a framework for fine mapping and subsequent cloning of major genes for important traits such as plant height and flowering time in sorghum.

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Identification of genetic factors controlling domestication-related traits in cowpea (Vigna unguiculata L. Walp)

10.1101/202044 ◽

2017 ◽

Cited By ~ 2

Author(s):

Sassoum Lo ◽

María Muñoz-Amatriaín ◽

Ousmane Boukar ◽

Ira Herniter ◽

Ndiaga Cisse ◽

...

Keyword(s):

Flowering Time ◽

Candidate Genes ◽

Vigna Unguiculata ◽

Recombinant Inbred Lines ◽

Warm Season ◽

Leaf Length ◽

Organ Size ◽

Chromosome 8 ◽

Nucleotide Polymorphisms ◽

Pod Shattering

AbstractCowpea (Vigna unguiculata L. Walp) is a warm-season legume with a genetically diverse gene-pool composed of wild and cultivated forms. Cowpea domestication involved considerable phenotypic changes from the wild progenitor, including reduction of pod shattering, increased organ size, and changes in flowering time. Little is known about the genetic basis underlying these changes. In this study, 215 recombinant inbred lines derived from a cross between a cultivated and a wild cowpea accession were used to evaluate nine domestication-related traits (pod shattering, peduncle length, flower color, flowering time, 100-seed weight, pod length, leaf length, leaf width and seed number per pod). A high-density genetic map containing 17,739 single nucleotide polymorphisms was constructed and used to identify 16 quantitative trait loci (QTL) for these nine domestication-related traits. Candidate genes underlying each of those 16 QTL were identified. Four regions with clusters of QTL were identified, including one on chromosome 8 related to increased organ size. This study provides new knowledge of the genomic regions controlling domestication-related traits in cowpea as well as candidate genes underlying those QTL. This information can help to exploit wild relatives in cowpea breeding programs.Key messageThis study identified regions of the cowpea genome that played an important role in cowpea domestication, including a hotspot region for increased organ size

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Quantitative trait loci and candidate genes associated with photoperiod sensitivity in lettuce (Lactuca spp.)

10.21203/rs.3.rs-290848/v1 ◽

2021 ◽

Author(s):

Rongkui Han ◽

Dean Lavelle ◽

Maria José Truco ◽

Richard Michelmore

Keyword(s):

Quantitative Trait Loci ◽

Flowering Time ◽

Quantitative Trait ◽

Recombinant Inbred Lines ◽

Genotyping By Sequencing ◽

Photoperiod Sensitivity ◽

Time Data ◽

Lactuca Serriola ◽

Long Day ◽

Trait Loci

Abstract The molecular mechanism of flowering time regulation in lettuce is of interest to both geneticists and breeders because of the extensive impact of this trait on agricultural production. Lettuce is a facultative long-day plant which changes in flowering time in response to photoperiod. Variations exist in both flowering time and the degree of photoperiod sensitivity among accessions of wild (Lactuca serriola) and cultivated (L. sativa) lettuce. An F6 population of 236 recombinant inbred lines (RILs) was previously developed from a cross between a late-flowering, photoperiod-sensitive L. serriola accession and an early-flowering, photoperiod-insensitive L. sativa accession. This population was planted under long-day (LD) and short-day (SD) conditions in a total of four field and screenhouse trials; the developmental phenotype was scored weekly in each trial. Using genotyping-by-sequencing (GBS) data of the RILs, quantitative trait loci (QTL) mapping revealed five flowering time QTLs that together explained more than 20% of the variation in flowering time under LD conditions. Using two independent statistical models to extract the photoperiod sensitivity phenotype from the LD and SD flowering time data, we identified an additional five QTLs that together explained more than 30% of the variation in photoperiod sensitivity in the population. Orthology and sequence analysis of genes within the nine QTLs revealed potential functional equivalents in the lettuce genome to the key regulators of flowering time and photoperiodism, FD and CONSTANS respectively, in Arabidopsis.

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Genomic Regions Controlling Yield-related Traits in Spring Wheat: A Mini Review and a Case Study for Rainfed Environments in Australia and China

10.21203/rs.3.rs-534020/v1 ◽

2021 ◽

Author(s):

Hui Liu ◽

Daniel Mullan ◽

Shancen Zhao ◽

Yong Zhang ◽

Jun Ye ◽

...

Keyword(s):

Candidate Genes ◽

Spring Wheat ◽

Genome Wide Association Study ◽

Single Gene ◽

Wheat Yield ◽

Genotyping By Sequencing ◽

Gene Clusters ◽

High Yield ◽

Wheat Varieties ◽

Rainfed Farming

Abstract Breeding high-yield wheat varieties performing well in target environment is economically important. This study conducted a mini review of genome-wide association study (GWAS) outcomes on wheat yield-related traits reported in recent years, and performed GWAS in six individual environments to identify major alleles and their candidate genes responsible for wheat yield-related traits in Australia and North China where rainfed farming system is adopted. A panel of 228 spring wheat varieties were used. A double digest restriction-site associated DNA (ddRAD) genotyping-by-sequencing (GBS) protocol was performed to generate single nucleotide polymorphism (SNP) marker data. A total of 223 significant marker-trait association (MTAs) for yield traits, and 46 candidate genes for the major or consistent MTAs were identified. A phenomenon seldom reported in previous studies was that MTA clustered chromosome segments and gene clusters responsible for the trait were found across the genome, which suggested that marker-assisted selection (MAS) or transgenic method targeting a single gene might not be as effective as MAS targeting a much larger genomic region (GR) where all the genes or gene clusters underlying the GR play important roles.

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Genome-Wide Association Study Reveals Candidate Genes for Flowering Time in Cowpea (Vigna unguiculata [L.] Walp.)

Frontiers in Genetics ◽

10.3389/fgene.2021.667038 ◽

2021 ◽

Vol 12 ◽

Author(s):

Dev Paudel ◽

Rocheteau Dareus ◽

Julia Rosenwald ◽

María Muñoz-Amatriaín ◽

Esteban F. Rios

Keyword(s):

Flowering Time ◽

Candidate Genes ◽

Vigna Unguiculata ◽

Association Studies ◽

Snp Markers ◽

Genome Wide Association ◽

Human Consumption ◽

Phenotypic Variance ◽

Genome Wide Association Studies ◽

Genome Wide

Cowpea (Vigna unguiculata [L.] Walp., diploid, 2n = 22) is a major crop used as a protein source for human consumption as well as a quality feed for livestock. It is drought and heat tolerant and has been bred to develop varieties that are resilient to changing climates. Plant adaptation to new climates and their yield are strongly affected by flowering time. Therefore, understanding the genetic basis of flowering time is critical to advance cowpea breeding. The aim of this study was to perform genome-wide association studies (GWAS) to identify marker trait associations for flowering time in cowpea using single nucleotide polymorphism (SNP) markers. A total of 368 accessions from a cowpea mini-core collection were evaluated in Ft. Collins, CO in 2019 and 2020, and 292 accessions were evaluated in Citra, FL in 2018. These accessions were genotyped using the Cowpea iSelect Consortium Array that contained 51,128 SNPs. GWAS revealed seven reliable SNPs for flowering time that explained 8–12% of the phenotypic variance. Candidate genes including FT, GI, CRY2, LSH3, UGT87A2, LIF2, and HTA9 that are associated with flowering time were identified for the significant SNP markers. Further efforts to validate these loci will help to understand their role in flowering time in cowpea, and it could facilitate the transfer of some of this knowledge to other closely related legume species.

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Fine mapping of a Phytophthora-resistance locus RpsGZ in soybean using Genotyping-by-Sequencing

10.21203/rs.2.12050/v1 ◽

2019 ◽

Author(s):

Bingzhi Jiang ◽

Yanbo Cheng ◽

Zhandong Cai ◽

Mu Li ◽

Ze Jiang ◽

...

Keyword(s):

Cell Death ◽

Candidate Genes ◽

Fine Mapping ◽

Average Distance ◽

Recombinant Inbred Lines ◽

Enrichment Analysis ◽

Genotyping By Sequencing ◽

Phytophthora Sojae ◽

Resistance Locus ◽

Phytophthora Root Rot

Abstract Background Phytophthora root rot (PRR), caused by Phytophthora sojae is one of the most important soil-borne diseases in many soybean-production regions in the world. Identification of resistant gene(s) and incorporating them into elite varieties are an effective way for breeding to prevent soybean from being harmed by this disease. A valuable mapping population of 228 F8:11 recombinant inbred lines (RILs) derived from a cross of resistant cultivar Guizao1 and susceptible cultivar BRSMG68 and a high-density genetic linkage map with an average distance of 0.81 centimorgan (cM) between adjacent bin markers in this population were used to map and explore the candidate genes. Results In this study, the PRR resistance in Guizao1 was controlled by a single Mendelian locus, and was fine mapped to a 460.702-kb genomic region on chromosome 3 that harbours 20 genes, including 8 disease resistance (R)-like genes in the reference Willliams 82 genome. These 8 candidate genes potentially involved in programmed cell death, cell death, apoptosis and ADP binding by adopting Gene Ontology (GO) enrichment analysis. Conclusions These findings of fine mapping of a novel Rps locus will serve as a basis for cloning, transferring of resistant genes and breeding of P. sojae resistant soybean cultivars through marker-assisted selection.

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QTL Analysis of Five Morpho-Physiological Traits in Bread Wheat Using Two Mapping Populations Derived from Common Parents

Genes ◽

10.3390/genes12040604 ◽

2021 ◽

Vol 12 (4) ◽

pp. 604

Author(s):

Paolo Vitale ◽

Fabio Fania ◽

Salvatore Esposito ◽

Ivano Pecorella ◽

Nicola Pecchioni ◽

...

Keyword(s):

Candidate Genes ◽

Recombinant Inbred Lines ◽

Snp Array ◽

Heading Date ◽

Tiller Number ◽

Genetic Maps ◽

Yield Potential ◽

Adaptation To Climate Change ◽

Map Resolution ◽

Mapping Populations

Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental population at early (F2 and F2-derived F3 families) and late (F6 and F7, recombinant inbred lines, RILs) generations to detect quantitative trait loci (QTLs) and search for candidate genes. A total of 176 and 178 lines were genotyped by the wheat Illumina 25K Infinium SNP array. The two genetic maps spanned 2486.97 cM and 3732.84 cM in length, for the F2 and RILs, respectively. QTLs explaining the highest phenotypic variation were found on chromosomes 2B, 2D, 5A, and 7D for HD and GH, whereas those for PH were found on chromosomes 4B and 4D. Several QTL detected in the early generations (i.e., PH and tiller number) were not detected in the late generations as they were due to dominance effects. Some of the identified QTLs co-mapped to well-known adaptive genes (i.e., Ppd-1, Vrn-1, and Rht-1). Other putative candidate genes were identified for each trait, of which PINE1 and PIF4 may be considered new for GH and TTN in wheat. The use of a large F2 mapping population combined with NGS-based genotyping techniques could improve map resolution and allow closer QTL tagging.

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High resolution mapping and candidate gene identification of downy mildew race 16 resistance in spinach

BMC Genomics ◽

10.1186/s12864-021-07788-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Gehendra Bhattarai ◽

Wei Yang ◽

Ainong Shi ◽

Chunda Feng ◽

Braham Dhillon ◽

...

Keyword(s):

Candidate Genes ◽

Downy Mildew ◽

Association Analysis ◽

Spinacia Oleracea ◽

Genotyping By Sequencing ◽

Significant Snps ◽

Snp Markers ◽

Resistance Locus ◽

Downy Mildew Resistance ◽

Mildew Resistance

Abstract Background Downy mildew, the most devastating disease of spinach (Spinacia oleracea L.), is caused by the oomycete Peronospora effusa [=P. farinosa f. sp. spinaciae]. The P. effusa shows race specificities to the resistant host and comprises 19 reported races and many novel isolates. Sixteen new P. effusa races were identified during the past three decades, and the new pathogen races are continually overcoming the genetic resistances used in commercial cultivars. A spinach breeding population derived from the cross between cultivars Whale and Lazio was inoculated with P. effusa race 16 in an environment-controlled facility; disease response was recorded and genotyped using genotyping by sequencing (GBS). The main objective of this study was to identify resistance-associated single nucleotide polymorphism (SNP) markers from the cultivar Whale against the P. effusa race 16. Results Association analysis conducted using GBS markers identified six significant SNPs (S3_658,306, S3_692697, S3_1050601, S3_1227787, S3_1227802, S3_1231197). The downy mildew resistance locus from cultivar Whale was mapped to a 0.57 Mb region on chromosome 3, including four disease resistance candidate genes (Spo12736, Spo12784, Spo12908, and Spo12821) within 2.69–11.28 Kb of the peak SNP. Conclusions Genomewide association analysis approach was used to map the P. effusa race 16 resistance loci and identify associated SNP markers and the candidate genes. The results from this study could be valuable in understanding the genetic basis of downy mildew resistance, and the SNP marker will be useful in spinach breeding to select resistant lines.

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