Genetic Architecture of Flowering Phenology in Cereals and Opportunities for Crop Improvement

Hill, Camilla Beate; Li, Chengdao

doi:10.3389/fpls.2016.01906

Cited by 91 publications

(69 citation statements)

References 201 publications

(254 reference statements)

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“…In barley, phenology genes that determine heading date and photoperiod sensitivity drive adaptation to different geographic environments and cropping systems (Andres and Coupland, 2012;Russell et al, 2016). Extensive research in the model plant Arabidopsis has revealed many of the mechanisms that control flowering (Bl€ umel et al, 2015;Hill and Li, 2016). However, little is known about how natural genetic variation within phenology genes impacts grain yield and adaptation in barley.…”

Section: Introductionmentioning

confidence: 99%

Hybridisation‐based target enrichment of phenology genes to dissect the genetic basis of yield and adaptation in barley

Hill

Angessa

McFawn

et al. 2018

Plant Biotechnology Journal

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Summary Barley ( Hordeum vulgare L.) is a major cereal grain widely used for livestock feed, brewing malts and human food. Grain yield is the most important breeding target for genetic improvement and largely depends on optimal timing of flowering. Little is known about the allelic diversity of genes that underlie flowering time in domesticated barley, the genetic changes that have occurred during breeding, and their impact on yield and adaptation. Here, we report a comprehensive genomic assessment of a worldwide collection of 895 barley accessions based on the targeted resequencing of phenology genes. A versatile target‐capture method was used to detect genome‐wide polymorphisms in a panel of 174 flowering time‐related genes, chosen based on prior knowledge from barley, rice and Arabidopsis thaliana . Association studies identified novel polymorphisms that accounted for observed phenotypic variation in phenology and grain yield, and explained improvements in adaptation as a result of historical breeding of Australian barley cultivars. We found that 50% of genetic variants associated with grain yield, and 67% of the plant height variation was also associated with phenology. The precise identification of favourable alleles provides a genomic basis to improve barley yield traits and to enhance adaptation for specific production areas.

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Section: Introductionmentioning

confidence: 99%

Hybridisation‐based target enrichment of phenology genes to dissect the genetic basis of yield and adaptation in barley

Hill

Angessa

McFawn

et al. 2018

Plant Biotechnology Journal

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“…Across all field trials, we identified 1,132 significant unique marker-trait associations (MTAs) (false discovery rate [FDR] of P < 0.05) for flowering time located within 327 unique genes with functional annotations, each explaining up to 18.7% of the phenotypic variation (S13 File, S18 Figure). These regions include known phenology-related genes, such as HvPPD-H1 , PHYTOCHROME C ( HvPhyC ), PROTEIN KINASE 2A ( HvCK2A ), HvADA2, PHYTOCHROME-ASSOCIATED PROTEIN 2 ( HvPAP2 ), and VERNALIZATION H1 ( HvVRN-H1 ) [4,10–12]. Furthermore, a total of 246 MTAs were considered to be ‘stable’, 76 MTAs were considered to be ‘consistent’, and 73 MTAs were considered to be ‘robust’ (S13 File).…”

Section: Resultsmentioning

confidence: 99%

“…Notably, we also detected novel associations with candidate phenology-related genes that were not included in the previous target-enrichment sequencing study [10] but that have annotations linking them to roles in flowering time regulation, including CCT and PRR motifs characteristic of key phenology genes such as HvCO1 , HvVRN-H2 , and HvPPD-H1 [4]. These genes included HORVU1Hr1G011030 and HORVU5Hr1G125620 (both annotated as COP1-interacting protein-related), HORVU2Hr1G055130 and HORVU7Hr1G044380 (both annotated as CONSTANS, CO-like, and TOC1 [CCT] motif family protein, and HORVU3Hr1G092330 and HORVU6Hr1G008870 (both annotated as pentatricopeptide repeat-containing protein).…”

Section: Resultsmentioning

confidence: 99%

“…Changes in global climate and short-term variations in growing environments pose unprecedented challenges to maintain and further enhance crop yields. Among other effects, climate change substantially alters phenological cycles, thereby posing a significant challenge to growers, who must modify crop management practices such as sowing dates in order to achieve optimal flowering times [4]. Conservation and maintenance of current crop genetic diversity for future breeding of new varieties is particularly important to help mitigate future adverse impacts of climate change on crop production.…”

Section: Introductionmentioning

confidence: 99%

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A global barley panel revealing genomic signatures of breeding in modern cultivars

Hill

Angessa

Zhang

et al. 2020

Preprint

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18The future of plant cultivar improvement lies in the evaluation of genetic resources from 19 currently available germplasm. Recent efforts in plant breeding have been aimed at 20 developing new and improved varieties from poorly adapted crops to suit local environments. 21 However, the impact of these breeding efforts is poorly understood. Here, we assess the 22 contributions of both historical and recent breeding efforts to local adaptation and crop 23 improvement in a global barley panel by analysing the distribution of genetic variants with 24 respect to geographic region or historical breeding category. By tracing the impact breeding 25 had on the genetic diversity of barley released in Australia, where the history of barley 26 production is relatively young, we identify 69 candidate regions within 922 genes that were 27 under selection pressure. We also show that modern Australian barley varieties exhibit 12% 28 higher genetic diversity than historical cultivars. Finally, field-trialling and phenotyping for 29 agriculturally relevant traits across a diverse range of Australian environments suggests that 30 genomic regions under strong breeding selection and their candidate genes are closely 31 associated with key agronomic traits. In conclusion, our combined dataset and germplasm 32 collection provide a rich source of genetic diversity that can be applied to understanding and 33 improving environmental adaptation and enhanced yields. 35Author summary 36 Today's gene pool of crop genetic diversity has been shaped during domestication and more 37 recently by breeding. Genetic diversity is vital for crop species to be able to adapt to 38 changing environments. There is concern that recent breeding efforts have eroded the genetic 39 diversity of many domesticated crops including barley. The present study assembled a global 40 panel of barley genotypes with a focus on historical and modern Australian varieties.41 Genome-wide data was used to detect genes that are thought to have been under selection 3 42 during crop breeding in Australian barley. The results demonstrate that despite being more 43 extensively bred, modern Australian barley varieties exhibit higher genetic diversity than 44 historical cultivars, countering the common perception that intensive breeding leads to 45 genetic erosion of adaptive diversity in modern cultivars. In addition, some loci (particularly 46 those related to phenology) were subject to selection during the introduction of other barley 47 varieties to Australia -these genes might continue to be important targets in breeding efforts 48 in the face of changing climatic conditions. 49 50 51The diversity of the existing genetic pool for commercially important plant species has been 52 shaped during plant domestication, human migration, varietal selection processes and, more 53 recently, breeding. However, there is concern that breeding efforts have eroded genetic 54 variation, thereby resulting in a narrow range of genotypes in the current gene pools of 55 domesticated crops [1...

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“…A long vegetative phase means later flowering, larger and more vegetative organs (such as leaves and roots), that results in high yield because it provides the plenty source for yield formation. However, crops in the field may not mature normally before winter and lose the yield if the vegetative phase is too long 4 . Balancing vegetative and reproductive growth will achieve high yield in a normal growth season.…”

Section: Introductionmentioning

confidence: 99%

FT/FD-GRF5 repression loop directs growth to increase soybean yield

Zhang

et al. 2018

Preprint

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28Major advances in crop yield are eternally needed to cope with population growth. To 29 balance vegetative and reproductive growth plays an important role in agricultural yield. 30To extend vegetative phase can increase crop yield, however, this strategy risks loss of 31 yield in the field as crops may not mature in time before winter come. Here, we identified 32 a repression feedback loop between GmFTL/GmFDL and GmGRF5-1 (Glycine-max-33 Flowering-Locus-T/Glycine-max-FDL and Glycine-max-GROWTH-REGULATING-34 FACTOR5-1), which functions as a pivotal regulator in balancing vegetative and 35 reproductive phases in soybean. GmFTL/GmFDL and GmGRF5-1 directly repress gene 36 expression each other. Additionally, GmGRF5-1 enhances vegetative growth by directly 37 enhancing expression of photosynthesis-and auxin synthesis-related genes. To 38 modulate the loop, such as fine-tuning GmFTL expression to trade-off vegetative and 39 reproductive growth, increases substantially soybean yield in the field. Our findings not 40 only uncover the mechanism balancing vegetative and reproductive growth, but open a 41 new window to improve crop yield. 42 43 48vegetative growth is closely related to reproductive growth. A long vegetative phase means 49 later flowering, larger and more vegetative organs (such as leaves and roots), that results in 50 high yield because it provides the plenty source for yield formation. However, crops in the 51 field may not mature normally before winter and lose the yield if the vegetative phase is too 52 long 4 . Balancing vegetative and reproductive growth will achieve high yield in a normal growth 53 season. 54 55 3 The transition from the vegetative to reproductive phase is regulated by a complex genetic 56 network that monitors and integrates both the plant developmental and environmental signals, 57 resulting in production of florigen Flowering Locus T (FT) 5,6 . The lower the florigen production, 58 the later the flowering and the higher the yield, and vice versa 3 . The FT dosage plays a key 59 role in the yield of tomato 7 and rice 8 . Not only function on flowering control, FT homologs also 60 contribute to the regulation of vegetative growth, such as tuberisation 9 , onion bulb formation 10 61 and sugar beet growth 11 . FT coordinates reproductive and vegetative growth in perennial 62 poplar 12 . Recently, FT was reported to regulate seed dormancy through Flowering Locus C 13 . 63FT, together with FD negatively correlates with leaf size as its overexpression leads to smaller 64 leaves and reduced expression leads to increased leaf size 6,14 . But, the mechanism of FT in 65 regulating the development and function of leaves is still uncovered. 66 67 GROWTH-REGULATING-FACTOR (GRF) family genes encode plant-specific transcriptional 68 factors, which are shown to bind DNA with a TGTCAGG cis-element to repress or activate the 69 expression of their target genes 15,16 . GRF5 is confirmed as a key regulator of leaf growth and 70 photosynthetic efficiency by enhancing cell division and chloroplast divi...

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Genetic Architecture of Flowering Phenology in Cereals and Opportunities for Crop Improvement

Cited by 91 publications

References 201 publications

Hybridisation‐based target enrichment of phenology genes to dissect the genetic basis of yield and adaptation in barley

Hybridisation‐based target enrichment of phenology genes to dissect the genetic basis of yield and adaptation in barley

A global barley panel revealing genomic signatures of breeding in modern cultivars

FT/FD-GRF5 repression loop directs growth to increase soybean yield

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