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Tiller angle (TA) strongly influences plant architecture and grain yield in cereals. However, the genetic basis of TA in wheat is largely unknown. We identified three TA-related quantitative trait loci (QTL). One of them was QTa.sau-2B-769, a major QTL localized on chromosome arm 2BL. QTa.sau-2B-769 was detected in seven environments, explaining 18.1%–51.1% of phenotypic variance. We developed a linked Kompetitive Allele-Specific Polymerase chain reaction (KASP) marker, KASP-AX-108792274, to further validate this locus in three additional populations in multiple environments. QTa.sau-2B-769 increased TA by up to 24.9% in these populations. There were significant and positive correlations between TA and flag leaf angle (FLANG). However, TA was not correlated with plant height or anthesis date, suggesting that expression of QTa.sau-2B-769 is independent of vernalization. TraesCS2B01G583800, a gene known to be involved in leaf angle regulation, was identified as the most likely candidate gene for QTa.sau-2B-769. These results enrich our understanding of the mechanisms regulating wheat TA at maturity and may support precise mapping and cloning of gene(s) underlying QTa.sau-2B-769.

Spikelet number per spike (SNS) is one of the crucial factors determining wheat yield. Thus, improving our understanding of the genes that regulate SNS could help develop higher-yielding wheat varieties. A genetic linkage map constructed using the GenoBaits Wheat 16K Panel and the 660K SNP array contained 5991 polymorphic SNP markers spanning 2813.26 cM. A total of twelve QTL for SNS were detected in the recombinant inbred line (RIL) populationmsf× Chuannong 16 (MC), and two of them, i.e.,QSns.sau-MC-3D.1andQSns.sau-MC-7A, were stably expressed.QSns.sau-MC-3D.1had high LOD values ranging from 4.99 to 11.06 and explained 9.71-16.75% of the phenotypic variation. Comparison ofQSns.sau-MC-3D.1with previously reported SNS QTL suggested that it is likely a novel one. A kompetitive allele-specific PCR (KASP) marker, KASP-10, tightly linked toQSns.sau-MC-3D.1was developed to successfully validate its effect in three segregated populations and a natural population. Genetic analysis indicated thatWHEAT ORTHOLOG OFAPO1(WAPO1) was a candidate gene forQSns.sau-MC-7A. The combined additive effect ofQSns.sau-MC-3D.1andWAP01had a great additive effect increasing SNS by 7.10%. In addition, our results suggested that SNS is not affected by 1BL/1RS translocations in the MC RIL population. Correlation analysis between two major QTL and other agronomic traits showed thatQSns.sau-MC-3D.1was likely independent of these agronomic traits. However, the H2 haplotype ofWAPO1may affect effective tiller number and plant height. This indicated that the breeding potential ofQSns.sau-MC-3D.1is better than that ofWAPO1. The geographical distribution ofQSns.nsau-MC-3D.1showed thatQSns.sau-MC-3D.1positive allele frequency was dominant in most wheat-producing regions of China and it has been positively selected among modern cultivars released in China since the 1940s. Two genes,TraesCS3D03G0222600andTraesCS3D03G0216800, associated with SNS development were predicted in the physical interval ofQSns.sau-MC-3D.1. qRT-PCR results of the two genes showed that only the expression level ofTraesCS3D03G0216800was significantly different between msf and CN16. These results enrich our understanding of the genetic basis of wheat SNS and will be useful for fine mapping and cloning of genes underlyingQSns.sau-MC-3D.1, and provide a basis for marker-assisted selection breeding.Author summaryIn this study, we identified two major QTL (QSns.sau-MC-3D.1andQSns.sau-MC-7A) in a RIL population.WAPO1was demonstrated to be the candidate gene forQSns.sau-MC-7A. QSns.sau-MC-3D.1was a novel and stably expressed QTL, and further confirmed in different genetic backgrounds. Our results further demonstrate thatQSns.sau-MC-3D.1has better breeding potential because of its no adverse effect on other agronomic traits thanWAPO1, and it has been positively selected during Chinese breeding programs since the 1940s. Taken together, the identification ofQSns.sau-MC-3D.1offers a promising resource to further increase wheat yields.

Background Improvement of wheat gercTriticum aestivum L.) yield could relieve global food shortages. Kernel size, as an important component of 1000-kernel weight (TKW), is always a significant consideration to improve yield for wheat breeders. Wheat related species possesses numerous elite genes that can be introduced into wheat breeding. It is thus vital to explore, identify, and introduce new genetic resources for kernel size from wheat wild relatives to increase wheat yield. Results In the present study, quantitative trait loci (QTL) for kernel length (KL) and width (KW) were detected in a recombinant inbred line (RIL) population derived from a cross between a wild emmer accession ‘LM001’ and a Sichuan endemic tetraploid wheat ‘Ailanmai’ using the Wheat 55 K single nucleotide polymorphism (SNP) array-based constructed linkage map and phenotype from six different environments. We identified eleven QTL for KL and KW including two major ones QKL.sicau-AM-3B and QKW.sicau-AM-4B, the positive alleles of which were from LM001 and Ailanmai, respectively. They explained 17.57 to 44.28% and 13.91 to 39.01% of the phenotypic variance, respectively. For these two major QTL, Kompetitive allele-specific PCR (KASP) markers were developed and used to successfully validate their effects in three F3 populations and two natural populations containing a panel of 272 Chinese wheat landraces and that of 300 Chinese wheat cultivars, respectively. QKL.sicau-AM-3B was located at 675.6–695.4 Mb on chromosome arm 3BL. QKW.sicau-AM-4B was located at 444.2–474.0 Mb on chromosome arm 4BL. Comparison with previous studies suggested that these two major QTL were likely new loci. Further analysis indicated that the positive alleles of QKL.sicau-AM-3B and QKW.sicau-AM-4B had a great additive effect increasing TKW by 6.01%. Correlation analysis between KL and other agronomic traits showed that KL was significantly correlated to spike length, length of uppermost internode, TKW, and flag leaf length. KW was also significantly correlated with TKW. Four genes, TRIDC3BG062390, TRIDC3BG062400, TRIDC4BG037810, and TRIDC4BG037830, associated with kernel development were predicted in physical intervals harboring these two major QTL on wild emmer and Chinese Spring reference genomes. Conclusions Two stable and major QTL for KL and KW across six environments were detected and verified in three biparental populations and two natural populations. Significant relationships between kernel size and yield-related traits were identified. KASP markers tightly linked the two major QTL could contribute greatly to subsequent fine mapping. These results suggested the application potential of wheat related species in wheat genetic improvement.

Barley shrunken endosperm mutants have been extensively reported. However, knowledge of the underlying molecular mechanisms of these mutants remains limited. Here, a pair of near isogenic lines (normal endosperm: Bowman and shrunken endosperm: sex1) was subjected to transcriptome analysis to identify mRNAs and lncRNAs related to endosperm development to further dissect its mechanism of molecular regulation. A total of 2123 (1140 up- and 983 down-regulated) unique differentially expressed genes (DEGs) were detected. Functional analyses showed that these DEGs were mainly involved in starch and sucrose metabolism, biosynthesis of secondary metabolites, and plant hormone signal transduction. A total of 343 unique target genes were identified for 57 differentially expressed lncRNAs (DE lncRNAs). These DE lncRNAs were mainly involved in glycerophospholipid metabolism, starch and sucrose metabolism, hormone signal transduction, and stress response. In addition, key lncRNAs were identified by constructing a co-expression network of the target genes of DE lncRNAs. Transcriptome results suggested that mRNA and lncRNA played a critical role in endosperm development. The shrunken endosperm in barley seems to be closely related to plant hormone signal transduction, starch and sucrose metabolism, and cell apoptosis. This study provides a foundation for fine mapping, elucidates the molecular mechanism of shrunken endosperm mutants, and also provides a reference for further studies of lncRNAs during the grain development of plants.

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.

Increasing wheat yield is essential in solving the global food shortage. The spikelet number per spike (SNS) is a primary factor that determines the kernel number per spike which has a great effect on wheat yield. Modern wheat breeding methods reduce the genetic diversity among cultivars, 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 high-density genetic map using the wheat 55K single nucleotide polymorphism (SNP) array. The linkage map revealed that 94.83% (6204) of the mapped markers had consistent genetic and physical chromosomal locations. 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 detected as the major and novel QTL with a large cumulative effect that increased SNS by 17.47%. Some development-related genes within the physical intervals of QSns.sau-AM-2B.3 and QSns.sau-AM-3B.2 were predicted to participate in spikelet growth, thereby affecting SNS. Genetic associations between SNS and other agronomic traits such as a significant and positive correlation between SNS and thousand kernel weight (TKW) were detected and analyzed. QTL analysis was also performed for other spike-related traits, including spike length (SL), kernel number per spike (KNS), kernel number per spikelet (KNL), and spike density (SD). QSns.sau-AM-2B.3 was co-located with QSl.sau-AM-2B in the interval between AX-111626925 and AX-111588559. Similarly, QKns.sau-AM-5B.1 was co-related with QKnl.sau-AM-5B.2 in the region between AX-108760512 and AX-110180251. This study demonstrates the feasibility of wheat 55K SNP array in genetic mapping of tetraploid wheat population and shows the potential application of wheat related species in wheat improvement programs.

The spikelet number per spike (SNS) is a primary factor determining 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 the wheat 55K single nucleotide polymorphism (SNP) array. The linkage map containing 1150 bin markers with a total genetic distance of 2411.8 cM was obtained. Based on phenotypic data from eight environments and best linear unbiased prediction (BLUP) values, five quantitative trait loci (QTL) for SNS were identified, explaining 6.71-29.40% of the phenotypic variation. Two of them, QSns.sau-AM-2B.3 and QSns.sau-AM-3B.2, were detected as the 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 corresponding QTL 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 wheat 55K SNP array developed for common wheat in genetic mapping of tetraploid population and shows the potential application of wheat related species in wheat improvement programs.