Interactions Among Multiple Quantitative Trait Loci Underlie Rhizome Development of Perennial Rice

Zhang, Fan; Wang, Kai; Rao, Jianglei; Cai, Zhongquan; Tao, Luwei; Yang, Fanyi; Yang, Jiangyi

doi:10.3389/fpls.2020.591157

Cited by 12 publications

(19 citation statements)

References 53 publications

(58 reference statements)

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“…In the present study, we substantially expanded the genetic repertoire for rhizome development. A recent manuscript ( Fan et al, 2020 ) identified over 10 loci related to rhizome growth, including five major-effect loci— qRED1.2 , qRED3.1 , qRED3.3 , qRED4.1 , and qRED4.2 , some of which are partially overlapped with two previously mapped loci determining the presence of rhizome, Rhz2 and Rhz3 ( Hu et al, 2003 ). Here, we identified 13 Rhz-regulating loci and as many as 51 QTLs controlling rhizome abundance.…”

Section: Discussionmentioning

confidence: 99%

“…Based on a complete simple sequence-repeat map, Hu et al (2003) identified two dominant-complementary loci, termed Rhz2 and Rhz3 , that predominantly control rhizomatousness in O. longistaminata , and the authors also revealed many QTLs affecting rhizome abundance ( Hu et al, 2003 ). Recently, through entire population genotyping mapping and selective genotyping mapping using three F 2 populations, over 10 major- or minor-effect rhizome-regulating QTLs were identified; however, none of these QTLs could be able to function alone, indicating that interactions among multiple QTLs are required for proper rhizome development ( Fan et al, 2020 ). Nevertheless, to our knowledge, no reports have detailed how the rhizome-related QTLs interact with each other.…”

Section: Introductionmentioning

confidence: 99%

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A Genetic Network Underlying Rhizome Development in Oryza longistaminata

Zhang

Huang

et al. 2022

Front. Plant Sci.

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The rhizome is an important organ through which many perennial plants are able to propagate vegetatively. Its ecological role has been thoroughly studied on many grass species while the underlying genetic basis is mainly investigated using a rhizomatous wild rice species—Oryza longistaminata. Previous studies have revealed that the rhizome trait in O. longistaminata is jointly controlled by multiple loci, yet how these loci interact with each other remains elusive. Here, an F2 population derived from Oryza sativa (RD23) and O. longistaminata was used to map loci that affect rhizome-related traits. We identified 13 major-effect loci that may jointly control rhizomatousness in O. longistaminata and a total of 51 quantitative trait loci (QTLs) were identified to affect rhizome abundance. Notably, some of these loci were found to have effects on more than one rhizome-related trait. For each trait, a genetic network was constructed according to the genetic expectations of the identified loci. Furthermore, to gain an overview of the genetic regulation on rhizome development, a comprehensive network integrating all these individual networks was assembled. This network consists of three subnetworks that control different aspects of rhizome expression. Judging from the nodes’ role in the network and their corresponding traits, we speculated that qRHZ-3-1, qRHZ-4, qRHI-2, and qRHI-5 are the key loci for rhizome development. Functional verification using rhizome-free recombinant inbred lines (RILs) suggested that qRHI-2 and qRHI-5, two multi-trait controlling loci that appeared to be critical in our network analyses, are likely both needed for rhizome formation. Our results provide more insights into the genetic basis of rhizome development and may facilitate identification of key rhizome-related genes.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A Genetic Network Underlying Rhizome Development in Oryza longistaminata

Zhang

Huang

et al. 2022

Front. Plant Sci.

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“…Previous genetic studies of perenniality in grasses have focused on morphological traits, most notably tiller and rhizome growth, and not the key phenotype of regrowth after senescence. Studies in rice ( Hu et al, 2003 ; Fan et al, 2020 ), sorghum ( Paterson et al, 1995 ; Kong et al, 2015 ), and maize ( Westerbergh and Doebley, 2004 ) have highlighted that rhizome development is a complex, multigenic trait that is influenced by the environment. Rhizomes are organs necessary for over-wintering in grasses ( Washburn et al, 2013 ) but since not all perennials must over-winter they may not be absolutely required for perennial regrowth.…”

Section: Discussionmentioning

confidence: 99%

“…Rhizomes are below-ground organs derived from stems that can store resources used for regrowth. Trait mapping studies in Oryza ( Hu et al, 2003 ; Fan et al, 2020 ), Sorghum ( Paterson et al, 1995 ; Kong et al, 2015 ), and Zea ( Westerbergh and Doebley, 2004 ) revealed QTL associated with the presence of rhizomes in F 2 progeny. These are important first steps but it remains unclear whether lines bred for rhizome formation will demonstrate perennial regrowth.…”

Section: Introductionmentioning

confidence: 99%

QTL Map of Early- and Late-Stage Perennial Regrowth in Zea diploperennis

et al. 2021

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Numerous climate change threats will necessitate a shift toward more sustainable agricultural practices during the 21st century. Conversion of annual crops to perennials that are capable of regrowing over multiple yearly growth cycles could help to facilitate this transition. Perennials can capture greater amounts of carbon and access more water and soil nutrients compared to annuals. In principle it should be possible to identify genes that confer perenniality from wild relatives and transfer them into existing breeding lines to create novel perennial crops. Two major loci controlling perennial regrowth in the maize relative Zea diploperennis were previously mapped to chromosome 2 (reg1) and chromosome 7 (reg2). Here we extend this work by mapping perennial regrowth in segregating populations involving Z. diploperennis and the maize inbreds P39 and Hp301 using QTL-seq and traditional QTL mapping approaches. The results confirmed the existence of a major perennial regrowth QTL on chromosome 2 (reg1). Although we did not observe the reg2 QTL in these populations, we discovered a third QTL on chromosome 8 which we named regrowth3 (reg3). The reg3 locus exerts its strongest effect late in the regrowth cycle. Neither reg1 nor reg3 overlapped with tiller number QTL scored in the same population, suggesting specific roles in the perennial phenotype. Our data, along with prior work, indicate that perennial regrowth in maize is conferred by relatively few major QTL.

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“…To our knowledge, the last genetic studies of perennial rye were at the methodological level of chromosome microscopy, but perenniality (and fertility) was also studied in other cereals (rice, sorghum, maize, wheat) and their perennial wild relatives by means of molecular markers [30][31][32][33][34][35][36] and sequence based genomics and transcriptomics [37][38][39][40]. All those studies showed that the genetics of perenniality was highly complex.…”

Section: Introductionmentioning

confidence: 99%

Perennial Rye: Genetics of Perenniality and Limited Fertility

Gruner

Miedaner

2021

Plants

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Perenniality, the ability of plants to regrow after seed set, could be introgressed into cultivated rye by crossing with the wild relative and perennial Secale strictum. However, studies in the past showed that Secale cereale × Secale strictum-derived cultivars were also characterized by reduced fertility what was related to so called chromosomal multivalents, bulks of chromosomes that paired together in metaphase I of pollen mother cells instead of only two chromosomes (bivalents). Those multivalents could be caused by ancient translocations that occurred between both species. Genetic studies on perennial rye are quite old and especially the advent of molecular markers and genome sequencing paved the way for new insights and more comprehensive studies. After a brief review of the past research, we used a basic QTL mapping approach to analyze the genetic status of perennial rye. We could show that for the trait perennation 0.74 of the genetic variance in our population was explained by additively inherited QTLs on chromosome 2R, 3R, 4R, 5R and 7R. Fertility on the other hand was with 0.64 of explained genetic variance mainly attributed to a locus on chromosome 5R, what was most probably the self-incompatibility locus S5. Additionally, we could trace the Z locus on chromosome 2R by high segregation distortion of markers. Indications for chromosomal co-segregation, like multivalents, could not be found. This study opens new possibilities to use perennial rye as genetic resource and for alternative breeding methods, as well as a valuable resource for comparative studies of perennation across different species.

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Interactions Among Multiple Quantitative Trait Loci Underlie Rhizome Development of Perennial Rice

Cited by 12 publications

References 53 publications

A Genetic Network Underlying Rhizome Development in Oryza longistaminata

A Genetic Network Underlying Rhizome Development in Oryza longistaminata

QTL Map of Early- and Late-Stage Perennial Regrowth in Zea diploperennis

Perennial Rye: Genetics of Perenniality and Limited Fertility

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