Identification of major quantitative trait loci for root diameter in synthetic hexaploid wheat under phosphorus-deficient conditions

Chromosome groups 5, 6 and 7 harbor major quantitative trait loci controlling root traits in bread wheat (Triticum aestivum L.)

Identifying genomic regions for root traits in bread wheat can help breeders develop climate-resilient and high-yielding wheat varieties with desirable root traits. This study used the recombinant inbred line (RIL) population of Synthetic W7984 × Opata M85 to identify quantitative trait loci (QTL) for different root traits such as rooting depth (RD), root dry mass (RM), total root length (RL), root diameter (Rdia) and root surface areas (RSA1 for coarse roots and RSA2 for fine roots) under controlled conditions in a semi-hydroponic system. We detected 14 QTL for eight root traits on nine wheat chromosomes; we discovered three QTL each for RD and RSA1, two QTL each for RM and RSA2, and one QTL each for RL, Rdia, specific root length and nodal root number per plant. The detected QTL were concentrated on chromosome groups 5, 6 and 7. The QTL for shallow RD (Q.rd.uwa.7BL: Xbarc50) and high RM (Q.rm.uwa.6AS: Xgwm334) were validated in two independent F₂ populations of Synthetic W7984 × Chara and Opata M85 × Cascade, respectively. Genotypes containing negative alleles for Q.rd.uwa.7BL had 52% shallower RD than other Synthetic W7984 × Chara population lines. Genotypes with the positive alleles for Q.rm.uwa.6AS had 31.58% higher RM than other Opata M85 × Cascade population lines. Further, we identified 21 putative candidate genes for RD (Q.rd.uwa.7BL) and 13 for RM (Q.rm.uwa.6AS); TraesCS6A01G020400, TraesCS6A01G024400 and TraesCS6A01G021000 identified from Q.rm.uwa.6AS, and TraesCS7B01G404000, TraesCS7B01G254900 and TraesCS7B01G446200 identified from Q.rd.uwa.7BL encoded important proteins for root traits. We found germin-like protein encoding genes in both Q.rd.uwa.7BL and Q.rm.uwa.6AS regions. These genes may play an important role in RM and RD improvement. The identified QTL, especially the validated QTL and putative candidate genes are valuable genetic resources for future root trait improvement in wheat.

Back to our roots: exploring the role of root morphology as a mediator of beneficial plant-microbe interactions

Plant breeding for belowground traits that have a positive impact on the rhizosphere microbiome is a promising strategy to sustainably improve crop yields. Root architecture and morphology are understudied plant breeding targets despite their potential to significantly shape microbial community structure and function in the rhizosphere. In this review, we explore the relationship between various root architectural and morphological traits and rhizosphere interactions, focusing on the potential of root diameter to impact the rhizosphere microbiome structure and function while discussing the potential biological and ecological mechanisms underpinning this process. In addition, we propose three future research avenues to drive this research area in an effort to unravel the effect of belowground traits on rhizosphere microbiology. This knowledge will pave the way for new plant breeding strategies that can be exploited for sustainable and high‐yielding crop cultivars.

Genome-Wide Association Study of Kernel Traits in Aegilops tauschii

Aegilops tauschii is the diploid progenitor of the D subgenome of hexaploid wheat (Triticum aestivum L.). Here, the phenotypic data of kernel length (KL), kernel width (KW), kernel volume (KV), kernel surface area (KSA), kernel width to length ratio (KWL), and hundred-kernel weight (HKW) for 223 A. tauschii accessions were gathered across three continuous years. Based on population structure analysis, 223 A. tauschii were divided into two subpopulations, namely T-group (mainly included A. tauschii ssp. tauschii accessions) and S-group (mainly included A. tauschii ssp. strangulata). Classifications based on cluster analysis were highly consistent with the population structure results. Meanwhile, the extent of linkage disequilibrium decay distance (r² = 0.5) was about 110 kb and 290 kb for T-group and S-group, respectively. Furthermore, a genome-wide association analysis was performed on these kernel traits using 6,723 single nucleotide polymorphism (SNP) markers. Sixty-six significant markers, distributed on all seven chromosomes, were identified using a mixed linear model explaining 4.82–13.36% of the phenotypic variations. Among them, 15, 28, 22, 14, 21, and 13 SNPs were identified for KL, KW, KV, KSA, KWL, and HKW, respectively. Moreover, six candidate genes that may control kernel traits were identified (AET2Gv20774800, AET4Gv20799000, AET5Gv20005900, AET5Gv20084100, AET7Gv20644900, and AET5Gv21111700). The transfer of beneficial genes from A. tauschii to wheat using marker-assisted selection will broaden the wheat D subgenome improve the efficiency of breeding.

Phenotypic and genetic variation in phosphorus-deficiency-tolerance traits in Chinese wheat landraces

BACKGROUND

Phosphorus deficiency is a major limiting factors for affecting crop production globally. To understand the genetic variation of phosphorus-deficiency-tolerance, a total of 15 seedling traits were evaluated among 707 Chinese wheat landraces under application of phosphorus (AP) and non-application of phosphorus (NP). A total of 18,594 single-nucleotide polymorphisms and 38,678 diversity arrays technology sequencing markers were used to detect marker-trait associations under AP and NP.

RESULTS

Top ten genotypes with extremely tolerance and bottommost ten genotypes with extremely sensitivity were selected from 707 Chinese wheat landraces for future breeding and genetic analysis. A total of 55 significant markers (81 marker-trait associations) for 13 traits by both CMLM and SUPER method. These were distributed on chromosomes 1A, 1B, 2A, 2B, 2D, 3A, 4B, 5A, 5B, 6A, 6B, 6D, 7A and 7B. Considering the linkage disequilibrium decay distance, 25 and 12 quantitative trait loci (QTL) were detected under AP and NP, respectively (9 QTL were specific to NP).

CONCLUSIONS

The extremely tolerant landraces could be used for breeding phosphorus-deficiency-tolerant cultivars. The QTL could be useful in wheat breeding through marker-assisted selection. Our findings provide new insight into the genetic analysis of P-deficiency-tolerance, and will be helpful for breeding P-deficiency-tolerant cultivars.

Discovering consensus genomic regions in wheat for root-related traits by QTL meta-analysis

Root system architecture is crucial for wheat adaptation to drought stress, but phenotyping for root traits in breeding programmes is difficult and time-consuming owing to the belowground characteristics of the system. Identifying quantitative trait loci (QTLs) and linked molecular markers and using marker-assisted selection is an efficient way to increase selection efficiency and boost genetic gains in breeding programmes. Hundreds of QTLs have been identified for different root traits in the last few years. In the current study, consensus QTL regions were identified through QTL meta-analysis. First, a consensus map comprising 7352 markers was constructed. For the meta-analysis, 754 QTLs were retrieved from the literature and 634 of them were projected onto the consensus map. Meta-analysis grouped 557 QTLs in 94 consensus QTL regions, or meta-QTLs (MQTLs), and 18 QTLs remained as singletons. The recently published genome sequence of wheat was used to search for gene models within the MQTL peaks. As a result, gene models for 68 of the 94 Root_MQTLs were found, 35 of them related to root architecture and/or drought stress response. This work will facilitate QTL cloning and pyramiding to develop new cultivars with specific root architecture for coping with environmental constraints.

Integration of Phenotype and Hormone Data during Adventitious Rooting in Carnation (Dianthus caryophyllus L.) Stem Cuttings

The rooting of stem cuttings is a highly efficient procedure for the vegetative propagation of ornamental plants. In cultivated carnations, an increased auxin level in the stem cutting base produced by active auxin transport from the leaves triggers adventitious root (AR) formation from the cambium. To provide additional insight into the physiological and genetic basis of this complex trait, we studied AR formation in a collection of 159 F1 lines derived from a cross between two hybrid cultivars (2003 R 8 and 2101-02 MFR) showing contrasting rooting performances. In three different experiments, time-series for several stem and root architectural traits were quantified in detail in a subset of these double-cross hybrid lines displaying extreme rooting phenotypes and their parental genotypes. Our results indicate that the water content and area of the AR system directly contributed to the shoot water content and shoot growth. Moreover, morphometric data and rooting quality parameters were found to be associated with some stress-related metabolites such as 1-aminocyclopropane-1-carboxylic acid (ACC), the ethylene precursor, and the conjugated auxin indol-3-acetic acid-aspartic acid (IAA-Asp).