Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding

Lovell, John T; Bentley, Nolan; Bhattarai, Gaurab; Jenkins, Jerry; Sreedasyam, Avinash; Alarcón, Yanina; Bock, Clive H.; Boston, Lori Beth; Carlson, Joseph W.; Cervantes, Kimberly; Clermont, Kristen; Duke, Sara E.; Krom, Nick; Kubenka, Keith; Mamidi, Sujan; Mattison, Christopher P.; Monteros, María J.; Pisani, Cristina; Plott, Christopher; Rajasekar, Shanmugam; Rhein, Hormat Shadgou; Rohla, Charles T.; Song, Mingzhou; Hilaire, Rolston St.; Shu, Shengqiang; Wells, Lance; Webber, Jenell; Heerema, Richard J.; Klein, Patricia E.; Conner, Patrick J.; Wang, Xinwang; Grauke, L.J.; Schmutz, Jeremy; Randall, Jennifer J.

doi:10.1038/s41467-021-24328-w

Cited by 68 publications

(57 citation statements)

References 87 publications

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“…With recent advances in long-read sequencing and assembly technologies, such structural variation is evident in chromosomal haplotype assemblies for polyploid and highly heterozygous genomes (e.g., refs. 32 , 44 , 46 ). Until recently, such high-quality genomes were primarily produced for inbred crop and genetic model species, but they are increasingly emerging for plant species outside these criteria (e.g., Lindenbergia , Acorus , Joinvillea , and Pharus ; https://phytozome-next.jgi.doe.gov/ogg/ ).…”

Section: What Do We Mean By a “Genome” In Plants? Why Are High-quality Genomes Needed?mentioning

confidence: 99%

Green plant genomes: What we know in an era of rapidly expanding opportunities

Kress

Soltis

Kersey

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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Green plants play a fundamental role in ecosystems, human health, and agriculture. As de novo genomes are being generated for all known eukaryotic species as advocated by the Earth BioGenome Project, increasing genomic information on green land plants is essential. However, setting standards for the generation and storage of the complex set of genomes that characterize the green lineage of life is a major challenge for plant scientists. Such standards will need to accommodate the immense variation in green plant genome size, transposable element content, and structural complexity while enabling research into the molecular and evolutionary processes that have resulted in this enormous genomic variation. Here we provide an overview and assessment of the current state of knowledge of green plant genomes. To date fewer than 300 complete chromosome-scale genome assemblies representing fewer than 900 species have been generated across the estimated 450,000 to 500,000 species in the green plant clade. These genomes range in size from 12 Mb to 27.6 Gb and are biased toward agricultural crops with large branches of the green tree of life untouched by genomic-scale sequencing. Locating suitable tissue samples of most species of plants, especially those taxa from extreme environments, remains one of the biggest hurdles to increasing our genomic inventory. Furthermore, the annotation of plant genomes is at present undergoing intensive improvement. It is our hope that this fresh overview will help in the development of genomic quality standards for a cohesive and meaningful synthesis of green plant genomes as we scale up for the future.

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Section: What Do We Mean By a “Genome” In Plants? Why Are High-quality Genomes Needed?mentioning

confidence: 99%

Green plant genomes: What we know in an era of rapidly expanding opportunities

Kress

Soltis

Kersey

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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“…The USDA-ARS Pecan Breeding program has been using these 14 nuclear and 3 plastid SSR markers to identify cultivars, hybrids, and unknown varieties. Recently, three of these SSR markers were used to identify F 1 progeny in a cross of "Lakota" × 87MX3-2.11, which was used for candidate gene identification [44]. Existing profiles from verified inventories will be useful in establishing additional methods of molecular verification [18].…”

Section: Discussionmentioning

confidence: 99%

“…Additional microsatellite markers should be selected for their distribution across all chromosomes and high nucleotide repeat numbers (tri and tetra). Next-generation sequencing technology provides a more efficient tool to quickly profile tree species with a greater resolution of interspecific hybridity, especially when their markers (SNPs) are aligned to an available chromosome-scale genome sequence [27,44]. However, SSR markers still have great utility for plant breeding programs and researchers who need markers that have high reproducibility, transferability between species, and platform independence.…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity Revealed by Microsatellites in Genus Carya

Wang¹,

Chatwin²,

Hilton³

et al. 2022

Forests

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The genus Carya consists of 17 species divided into 3 sections: Carya or the true hickories, Apocarya or the pecan hickories, and Sinocarya or the Asian hickories. Interspecific hybrids exist and have been used in pecan cultivar development. Nuclear and plastid microsatellite or SSR markers have been useful in distinguishing species, sections, and populations. They provide evidence for hybridity between species and can confirm heredity within crosses. As more sophisticated methods of genomic evaluation are cooperatively developed for use in pecan breeding and selection, the use of these methods will be supplemented and informed by the lessons provided by microsatellite markers, as interpreted across broad germplasm collections. In this study, over 400 Carya accessions from diverse diploid and tetraploid taxa and their interspecific hybrids, maintained at the USDA National Collection of Genetic Resources for Carya (NCGR-Carya), were analyzed using 14 nuclear and 3 plastid microsatellite markers. Principal coordinate analysis showed clear taxonomic classifications at multiple taxonomic levels along with patterns of interspecific hybridity. Evidence was also found for genetic differences associated with geographic distribution. The results indicate that this group of markers is useful in examining and characterizing populations and hybrids in the genus Carya and may help delineate the composition of a core collection to help characterize the NCGR-Carya repository collection for use in its pecan breeding program. The SSR fingerprints of the inventories of the USDA NCGR-Carya repository can also be used as a reference for identifying unknown pecan trees for growers.

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“…In this study, 32 SPL genes were identified in the pecan genome, which was two more SPL genes than what was found in previous studies. We also identified the SPL gene family of pecan from the newly released genome ( https://phytozome-next.jgi.doe.gov/info/CillinoinensisPawnee_v1_1 ) ( Lovell et al, 2021 ). The number of SPL gene family members was found to be the same in the two versions of the pecan genome ( Table S8 ).…”

Section: Discussionmentioning

confidence: 99%

Characterization and expression analysis of the SPL gene family during floral development and abiotic stress in pecan (Carya illinoinensis)

Wang

Lin

et al. 2021

PeerJ

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SQUAMOSA promoter binding protein-like (SPL) genes are a type of plant-specific transcription factors that play crucial roles in the regulation of phase transition, floral transformation, fruit development, and various stresses. Although SPLs have been characterized in several model species, no systematic analysis has been studied in pecans, an important woody oil tree species. In this study, a total of 32 SPL genes (CiSPLs) were identified in the pecan genome. After conducting phylogenetic analysis of the conserved SBP proteins from Arabidopsis, rice, and poplar, the CiSPLs were separated into eight subgroups. The CiSPL genes within the same subgroup contained very similar exon-intron structures and conserved motifs. Nine segmentally duplicated gene pairs in the pecan genome and 16 collinear gene pairs between the CiSPL and AtSPL genes were identified. Cis-element analysis showed that CiSPL genes may regulate plant meristem differentiation and seed development, participate in various biological processes, and respond to plant hormones and environmental stresses. Therefore, we focused our study on the expression profiles of CiSPL genes during flower and fruit development. Most of the CiSPL genes were predominantly expressed in buds and/or female flowers. Additionally, quantitative real time PCR (qRT-PCR) analyses confirmed that CiSPL genes showed distinct spatiotemporal expression patterns in response to drought and salt treatments. The study provides foundation for the further exploration of the function and evolution of SPL genes in pecan.

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Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding

Cited by 68 publications

References 87 publications

Green plant genomes: What we know in an era of rapidly expanding opportunities

Green plant genomes: What we know in an era of rapidly expanding opportunities

Genetic Diversity Revealed by Microsatellites in Genus Carya

Characterization and expression analysis of the SPL gene family during floral development and abiotic stress in pecan (Carya illinoinensis)

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