WAPO-A1 is the causal gene of the 7AL QTL for spikelet number per spike in wheat

Improving our understanding of the genes regulating grain yield can contribute to the development of more productive wheat varieties. Previously, a highly significant QTL affecting spikelet number per spike (SNS), grain number per spike (GNS) and grain yield was detected on chromosome arm 7AL in multiple genome-wide association studies. Using a high-resolution genetic map, we established that the A-genome homeolog of WHEAT ORTHOLOG OF APO1 (WAPO-A1) was a leading candidate gene for this QTL. Using mutants and transgenic plants, we demonstrate in this study that WAPO-A1 is the causal gene underpinning this QTL. Loss-of-function mutants wapo-A1 and wapo-B1 showed reduced SNS in tetraploid wheat, and the effect was exacerbated in wapo1 combining both mutations. By contrast, spikes of transgenic wheat plants carrying extra copies of WAPO-A1 driven by its native promoter had higher SNS, a more compact spike apical region and a smaller terminal spikelet than the wild type. Taken together, these results indicate that WAPO1 affects SNS by regulating the timing of terminal spikelet formation. Both transgenic and wapo1 mutant plants showed a wide range of floral abnormalities, indicating additional roles of WAPO1 on wheat floral development. Previously, we found three widespread haplotypes in the QTL region (H1, H2 and H3), each associated with particular WAPO-A1 alleles. Results from this and our previous study, show that the WAPO-A1 allele in the H1 haplotype (115-bp deletion in the promoter) is expressed at significantly lower levels in the developing spikes than the alleles in the H2 and H3 haplotypes, resulting in reduced SNS. Field experiments also showed that the H2 haplotype is associated with the strongest effects in increasing SNS and GNS (H2>H3>H1). The H2 haplotype is already present in most modern common wheat varieties but is rare in durum wheat, where it might be particularly useful to improve grain yield.

Analysis of Genetic Regions Related to Field Grain Number per Spike From Chinese Wheat Founder Parent Linfen 5064

Wheat founder parents have been important in the development of new wheat cultivars. Understanding the effects of specific genome regions on yield-related traits in founder variety derivatives can enable more efficient use of these genetic resources through molecular breeding. In this study, the genetic regions related to field grain number per spike (GNS) from the founder parent Linfen 5064 were analyzed using a doubled haploid (DH) population developed from a cross between Linfen 5064 and Nongda 3338. Quantitative trait loci (QTL) for five spike-related traits over nine experimental locations/years were identified, namely, total spikelet number per spike (TSS), base sterile spikelet number per spike (BSSS), top sterile spikelet number per spike (TSSS), fertile spikelet number per spike (FSS), and GNS. A total of 13 stable QTL explaining 3.91–19.51% of the phenotypic variation were found. The effect of six of these QTL, Qtss.saw-2B.1, Qtss.saw-2B.2, Qtss.saw-3B, Qfss.saw-2B.2, Qbsss.saw-5A.1, and Qgns.saw-1A, were verified by another DH population (Linfen 5064/Jinmai 47), which showed extreme significance (P < 0.05) in more than three environments. No homologs of reported grain number-related from grass species were found in the physical regions of Qtss.saw-2B.1 and Qtss.saw-3B, that indicating both of them are novel QTL, or possess novel-related genes. The positive alleles of Qtss.saw-2B.2 from Linfen 5064 have the larger effect on TSS (3.30%, 0.62) and have 66.89% in Chinese cultivars under long-term artificial selection. This study revealed three key regions for GNS in Linfen 5064 and provides insights into molecular marker-assisted breeding.

The 55K SNP-Based Exploration of QTLs for Spikelet Number Per Spike in a Tetraploid Wheat (Triticum turgidum L.) Population: Chinese Landrace “Ailanmai” × Wild Emmer

Spikelet number per spike (SNS) is the primary factor that determines wheat yield. Common wheat breeding reduces the genetic diversity among elite germplasm resources, leading to a detrimental effect on future wheat production. It is, therefore, necessary to explore new genetic resources for SNS to increase wheat yield. A tetraploid landrace “Ailanmai” × wild emmer wheat recombinant inbred line (RIL) population was used to construct a genetic map using a wheat 55K single- nucleotide polymorphism (SNP) array. The linkage map containing 1,150 bin markers with a total genetic distance of 2,411.8 cm was obtained. Based on the phenotypic data from the eight environments and best linear unbiased prediction (BLUP) values, five quantitative trait loci (QTLs) for SNS were identified, explaining 6.71–29.40% of the phenotypic variation. Two of them, QSns.sau-AM-2B.2 and QSns.sau-AM-3B.2, were detected as a major and novel QTL. Their effects were further validated in two additional F2 populations using tightly linked kompetitive allele-specific PCR (KASP) markers. Potential candidate genes within the physical intervals of the corresponding QTLs were predicted to participate in inflorescence development and spikelet formation. Genetic associations between SNS and other agronomic traits were also detected and analyzed. This study demonstrates the feasibility of the wheat 55K SNP array developed for common wheat in the genetic mapping of tetraploid population and shows the potential application of wheat-related species in wheat improvement programs.

WAPO-A1 is the causal gene of the 7AL QTL for spikelet number per spike in wheat

Improving our understanding of the genes regulating grain yield can contribute to the development of more productive wheat varieties. Previously, a highly significant QTL affecting spikelet number per spike (SNS), grain number per spike (GNS) and grain yield was detected on chromosome arm 7AL in multiple genome-wide association studies. Using a high?resolution genetic map, we established that the A-genome homeolog of WHEAT ORTHOLOG OF APO1 ( WAPO-A1 ) was a leading candidate gene for this QTL. Using mutants and transgenic plants, we demonstrate in this study that WAPO-A1 is the causal gene underpinning this QTL. Loss-of-function mutants wapo-A1 and wapo-B1 showed reduced SNS in tetraploid wheat, and the effect was exacerbated in wapo1 combining both mutations. By contrast, spikes of transgenic wheat plants carrying extra copies of WAPO-A1 driven by its native promoter had higher SNS, a more compact spike apical region and a smaller terminal spikelet than the wild type. Taken together, these results indicate that WAPO1 affects SNS by regulating the timing of terminal spikelet formation. Both transgenic and wapo1 mutant plants showed a wide range of floral abnormalities, indicating additional roles of WAPO1 on wheat floral development. Previously, we found three widespread haplotypes in the QTL region (H1, H2 and H3), each associated with particular WAPO-A1 alleles. Integrating results from this study and previous findings, we show that the WAPO-A1 allele in the H1 haplotype (115-bp deletion in the promoter) is expressed at significantly lower levels in the developing spikes than the alleles in the H2 and H3 haplotypes, resulting in reduced SNS. Field experiments also showed that the H2 haplotype is associated with the strongest effects in increasing SNS and GNS (H2>H3>H1). The H2 haplotype is already present in most modern common wheats, so it might be particularly useful in durum wheat where H2 is rare.

QTL mapping for grain yield and three yield components in a population derived from two high-yielding spring wheat cultivars

Key message Four genomic regions on chromosomes 4A, 6A, 7B, and 7D were discovered, each with multiple tightly linked QTL (QTL clusters) associated with two to three yield components. The 7D QTL cluster was associated with grain yield, fertile spikelet number per spike, thousand kernel weight, and heading date. It was located in the flanking region of FT-D1, a homolog gene of Arabidopsis FLOWERING LOCUS T, a major gene that regulates wheat flowering. Abstract Genetic manipulation of yield components is an important approach to increase grain yield in wheat (Triticum aestivum). The present study used a mapping population comprised of 181 doubled haploid lines derived from two high-yielding spring wheat cultivars, UI Platinum and LCS Star. The two cultivars and the derived population were assessed for six traits in eight field trials primarily in Idaho in the USA. The six traits were grain yield, fertile spikelet number per spike, productive tiller number per unit area, thousand kernel weight, heading date, and plant height. Quantitative Trait Locus (QTL) analysis of the six traits was conducted using 14,236 single-nucleotide polymorphism (SNP) markers generated from the wheat 90 K SNP and the exome and promoter capture arrays. Of the 19 QTL detected, 14 were clustered in four chromosomal regions on 4A, 6A, 7B and 7D. Each of the four QTL clusters was associated with multiple yield component traits, and these traits were often negatively correlated with one another. As a result, additional QTL dissection studies are needed to optimize trade-offs among yield component traits for specific production environments. Kompetitive allele-specific PCR markers for the four QTL clusters were developed and assessed in an elite spring wheat panel of 170 lines, and eight of the 14 QTL were validated. The two parents contain complementary alleles for the four QTL clusters, suggesting the possibility of improving grain yield via genetic recombination of yield component loci.

Identification and Validation of a Novel Locus Controlling Spikelet Number in Bread Wheat (Triticum aestivum L.)

Spikelet number is an important target trait for wheat yield improvement. Thus, the identification and verification of novel quantitative trait locus (QTL)/genes controlling spikelet number are essential for dissecting the underlying molecular mechanisms and hence for improving grain yield. In the present study, we constructed a high-density genetic map for the Kechengmai1/Chuanmai42 doubled haploid (DH) population using 13,068 single-nucleotide polymorphism (SNP) markers from the Wheat 55K SNP array. A comparison between the genetic and physical maps indicated high consistence of the marker orders. Based on this genetic map, a total of 27 QTLs associated with total spikelet number per spike (TSN) and fertile spikelet number per spike (FSN) were detected on chromosomes 1B, 1D, 2B, 2D, 3D, 4A, 4D, 5A, 5B, 5D, 6A, 6B, and 7D in five environments. Among them, five QTLs on chromosome 2D, 3D, 5A, and 7D were detected in multiple environments and combined QTL analysis, explaining the phenotypic variance ranging from 3.64% to 23.28%. Particularly, QTsn/Fsn.cib-3D for TSN and FSN [phenotypic variation explained (PVE) = 5.97–23.28%, limit of detection (LOD) = 3.73–18.51] is probably a novel locus and located in a 4.5-cM interval on chromosome arm 3DL flanking by the markers AX-110914105 and AX-109429351. This QTL was further validated in other two populations with different genetic backgrounds using the closely linked Kompetitive Allele-Specific PCR (KASP) marker KASP_AX-110914105. The results indicated that QTsn/Fsn.cib-3D significantly increased the TSN (5.56–7.96%) and FSN (5.13–9.35%), which were significantly correlated with grain number per spike (GNS). We also preliminary analyzed the candidate genes within this locus by sequence similarity, spatial expression patterns, and collinearity analysis. These results provide solid foundation for future fine mapping and cloning of QTsn/Fsn.cib-3D. The developed and validated KASP markers could be utilized in molecular breeding aiming to increase the grain yield in wheat.

Linkage mapping identifies a non-synonymous mutation in FLOWERING LOCUS T (FT-B1) increasing spikelet number per spike

Total spikelet number per spike (TSN) is a major component of spike architecture in wheat (Triticumaestivum L.). A major and consistent quantitative trait locus (QTL) was discovered for TSN in a doubled haploid spring wheat population grown in the field over 4 years. The QTL on chromosome 7B explained up to 20.5% of phenotypic variance. In its physical interval (7B: 6.37–21.67 Mb), the gene FLOWERINGLOCUST (FT-B1) emerged as candidate for the observed effect. In one of the parental lines, FT-B1 carried a non-synonymous substitution on position 19 of the coding sequence. This mutation modifying an aspartic acid (D) into a histidine (H) occurred in a highly conserved position. The mutation was observed with a frequency of ca. 68% in a set of 135 hexaploid wheat varieties and landraces, while it was not found in other plant species. FT-B1 only showed a minor effect on heading and flowering time (FT) which were dominated by a major QTL on chromosome 5A caused by segregation of the vernalization gene VRN-A1. Individuals carrying the FT-B1 allele with amino acid histidine had, on average, a higher number of spikelets (15.1) than individuals with the aspartic acid allele (14.3) independent of their VRN-A1 allele. We show that the effect of TSN is not mainly related to flowering time; however, the duration of pre-anthesis phases may play a major role.

The Wheat 55K SNP-Based Exploration of Loci for Spikelet Number Per Spike From a Tetraploid Wheat (Triticum Turgidum L.) Recombinant Inbred Line Population Derived From a Chinese Landrace ‘ailanmai’ and a Wild Emmer Accession

Background: Increasing wheat yield is an urgent task to solve the global food shortage. Spikelet number per spike (SNS) is a key factor in determining kernel number per spike which has a great effect on wheat grain yield. However, modern wheat breeding narrows genetic diversity among cultivars leading to a detrimental effect on future wheat improvement. It is thus of great significance to explore new genetic resources for SNS to increase wheat yield.Results: A tetraploid landrace ‘Ailanmai’ × wild emmer wheat recombinant inbred line (RIL) population was used to construct a high-density genetic map using the wheat 55K single nucleotide polymorphism (SNP) array. The results showed that 94.83% (6204) of the mapped markers had consistent genetic and physical chromosomal locations. Subsequently, fourteen quantitative trait loci (QTL) for SNS explaining 4.23-27.26% of the phenotypic variation were identified. QSns.sau-AM-2B.3 and QSns.sau-AM-3B.2 were considered as major and novel QTL and their combination had the largest effect and increased SNS by 17.47%. In the physical intervals of QSns.sau-AM-2B.3 and QSns.sau-AM-3B.2, some development-related genes were predicted to participate in the spikelet growth and affect SNS. Additionally, significant correlations between SNS and other agronomic traits like significant and positive correlation between SNS and thousand kernel weight were detected and analyzed. Conclusions: Our study demonstrated the feasibility of wheat 55K SNP array in genetic mapping of tetraploid wheat and provided an example of exploring outstanding genetic resources from wheat related species for further utilization in common wheat improvement.

The wheat 55K SNP-based exploration of loci for spikelet number per spike from a tetraploid wheat (Triticum turgidum L.) recombinant inbred line population derived from a Chinese landrace ‘Ailanmai’ and a wild emmer accession

Spikelet number per spike (SNS) is a key factor in determining kernel number per spike which has a great effect on wheat grain yield. Modern wheat breeding narrows genetic diversity among cultivars leading to a detrimental effect on future wheat improvement. It is thus of great significance to explore new genetic resources for SNS to increase wheat yield. Here, a tetraploid landrace ‘Ailanmai’ × wild emmer wheat recombinant inbred line (RIL) population was used to construct a high-density genetic map using the wheat 55K single nucleotide polymorphism (SNP) array. Our results showed that the genetic and physical locations of 94.83% (6204) of the mapped markers were consistent. Subsequently, fourteen quantitative trait loci (QTL) for SNS explaining 4.23-27.26% of the phenotypic variation were identified. QSns.sau-AM-2B.3 and QSns.sau-AM-3B.2 were considered as major and novel QTL and their combination had the largest effect and increased SNS by 17.47%. In the physical intervals of QSns.sau-AM-2B.3 and QSns.sau-AM-3B.2, some development-related genes were predicted to participate in the spikelet growth and affect SNS. Additionally, significant correlations between SNS and other agronomic traits like significant and positive correlation between SNS and thousand kernel weight were detected and analyzed. Our findings demonstrated the feasibility of wheat 55K SNP array in genetic mapping of tetraploid wheat and provided an example of exploring outstanding genetic resources from wheat related species for further utilization in common wheat improvement.Key messageThe wheat 55K SNP array was firstly and successfully applied to construct a genetic map and explore two major and novel QTL for SNS in a tetraploid wheat RIL population.

Heterosis manifestations for spike productivity traits in durum wheat

The aim of the study is to investigate the heterosis manifestations in durum wheat for quantitative traits related to spike productivity. Diallel cross includes five modern varieties of durum wheat: Victoria (BG), Deni (BG), Superdur, Progress (BG), Predel (BG). The heterosis manifestations of the ten crosses are traced for the traits: spikelet number per spike, number of kernel per spike, grain weight per spike and thousand kernel weight. The experiment is conducted in the 2014-2016 period in the experimental field of FCI- Chirpan. Standard technology for the cultivation of durum wheat is applied. The trials are organized in a randomized block design with three replications. Of each replication 30 plants are randomly picked and harvested for biometric analysis. The mean values by years from the F1 spike biometric measurements are included in the statistical analysis to determine the mid parent and better parent heterosis. For spikelet number per spike, seven crosses show high parent heterosis in the first year, four in the second and six in the third year. In all years, hybrids with a variety of Victoria have more spikelet number per spike and show better parent heterosis. For the trait kernel number per spike it is observed that combinations with Deni variety in most cases have better parent heterosis. In all years, the cross Superdur x Predel indicates high parent heterosis for this trait. For grain weight per spike most of the combinations exhibit high levels of better parent heterosis. When the Deni variety is used as female parent, all hybrid combinations show high levels of heterosis for the trait grain weight per spike. In regard to the thousand kernel weight different heterosis levels are observed, with only negative values in the first year. In the other two years in hybrid combinations there is positive heterosis in one year and negative in another year. The participation of the Deni variety in hybrid combinations leads to better parent heterosis for this trait. The data allow the use of these crosses directly in the breeding of durum wheat to increase individual traits and/or increase productivity.