Tetraploid Parents Research Articles

APIS: an updated parentage assignment software managing triploids induced from diploid parents.

In aquaculture, sterile triploids are commonly used for production as sterility gives them potential gains in growth, yields, and quality. However, they cannot be reproduced, and DNA parentage assignment to their diploid or tetraploid parents is required to estimate breeding values for triploid phenotypes. No publicly available software has the ability to assign triploids to their parents. Here, we updated the R package APIS to support triploids induced from diploid parents. First, we created new exclusion and likelihood tables that account for the double allelic contribution of the dam and the recombination that can occur during female meiosis. As the effective recombination rate of each marker with the centromere is usually unknown, we set it at 0.5 and found that this value maximizes the assignment rate even for markers with high or low recombination rates. The number of markers needed for a high true assignment rate did not strongly depend on the proportion of missing parental genotypes. The assignment power was however affected by the quality of the markers (minor allele frequency, call rate). Altogether, 96-192 SNPs were required to have a high parentage assignment rate in a real rainbow trout dataset of 1,232 triploid progenies from 288 parents. The likelihood approach was more efficient than exclusion when the power of the marker set was limiting. When more markers were used, exclusion was more advantageous, with sensitivity reaching unity, very low false discovery rate (<0.01), and excellent specificity (0.96-0.99). Thus, APIS provides an efficient solution to assign triploids to their diploid parents.

Dosage effect genes modulate grain development in synthesized Triticum durum-Haynaldia villosa allohexaploid

Polyploidization in plants often leads to increased cell size and grain size, which may be affected by the increased genome dosage and transcription abundance. The synthesized Triticum durum (AABB)-Haynaldia villosa (VV) amphiploid (AABBVV) has significantly increased grain size, especially grain length, than the tetraploid and diploid parents. To investigate how polyploidization affects grain development at the transcriptional level, we perform transcriptome analysis using the immature seeds of T. durum, H. villosa, and the amphiploid. The dosage effect genes are contributed more by differentially expressed genes from genome V of H. villosa. The dosage effect genes overrepresent grain development-related genes. Interestingly, the vernalization gene TaVRN1 is among the positive dosage effect genes in the T. durum‒H. villosa and T. turgidum‒Ae. tauschii amphiploids. The expression levels of TaVRN1 homologs are positively correlated with the grain size and weight. The TaVRN1-B1 or TaVRN1-D1 mutation shows delayed florescence, decreased cell size, grain size, and grain yield. These data indicate that dosage effect genes could be one of the important explanations for increased grain size by regulating grain development. The identification and functional validation of dosage effect genes may facilitate the finding of valuable genes for improving wheat yield.

Cannabis Triploids Exhibit Reduced Fertility and Similar Growth and Flower Production Compared to Diploids

Cannabis (Cannabis sativa) grown for flowers containing cannabinoids requires all female plants, which are susceptible to seed set from exposure to pollen. Created triploids demonstrated reduced seed production compared with diploids in field and greenhouse studies in which plants were challenged with pollen from males. In the field, seed production as a percent of floral biomass ranged from 6.7% to 18.0% for triploids and from 52.6% to 57.1% for diploids. The photoperiod-insensitive triploid genotype ‘Purple Star’ × ‘Wilhelmina’ had 98.5% fewer filled (containing a developed embryo) seeds than the photoperiod-insensitive diploid genotype ‘Tsunami’ × ‘Wilhelmina’. In the greenhouse, triploid ‘Wife’ had 99.5% fewer filled seeds than diploid ‘Wife’. Plant growth and flower production were similar with eight triploid and seven diploid genotypes evaluated over three greenhouse studies. There were a few superior triploid and diploid genotypes; however, their performance was more likely attributable to the parental cultivar combination than ploidy level. The optimal cross direction for producing triploid seed in large quantities is tetraploid × diploid because the diploid × tetraploid cross exhibits triploid block caused by endosperm paternal excess. Colchicine-induced tetraploid parent plants should be tested over a prolonged period to eliminate cryptic chimeral mixoploids or tetraploid plants should be derived from seed produced by crossing two colchicine-induced putative tetraploid plants to ensure that seeds from tetraploid × diploid crosses will be triploid. The latter approach is necessary for photoperiod-insensitive cultivars because a prolonged period of ploidy testing is not possible for these plants. These findings indicate that triploid plants have significantly reduced fertility and are a suitable alternative to diploids in situations in which pollen exposure is possible.

Inheritance pattern of tetraploids pummelo, mandarin, and their interspecific hybrid sour orange is highly influenced by their phylogenomic structure.

Citrus polyploidy is associated with a wide range of morphological, genetic, and physiological changes that are often advantageous for breeding. Citrus triploid hybrids are very interesting as new seedless varieties. However, tetraploid rootstocks promote adaptation to different abiotic stresses and promote resilience. Triploid and tetraploid hybrids can be obtained through sexual hybridizations using tetraploid parents (2x × 4x, 4x × 2x, or 4x × 4x), but more knowledge is needed about the inheritance pattern of tetraploid parents to optimize the efficiency of triploid varieties and tetraploid rootstock breeding strategies. In this work, we have analyzed the inheritance pattern of three tetraploid genotypes: 'Chandler' pummelo (Citrus maxima) and 'Cleopatra' mandarin (Citrus reticulata), which represent two clear examples of autotetraploid plants constituted by the genome of a single species, and the 'Sevillano' sour orange, which is an allotetraploid interspecific hybrid between C. maxima and C. reticulata. Polymorphic simple sequence repeat (SSR) and single-nucleotide polymorphism (SNP) markers were used to estimate parental heterozygosity restitution, and allele frequencies for centromeric loci were used to calculate the preferential pairing rate related to the proportion of disomic and tetrasomic segregation. The tetraploid pummelo and mandarin displayed tetrasomic segregation. Sour orange evidenced a clear intermediate inheritance for five of the nine chromosomes (1, 2, 5, 7, and 8), a slight tendency toward tetrasomic inheritance on chromosome 3, and intermediate inheritance with a tendency toward disomy for chromosomes 4, 6, and 9. These results indicate that the interspecific versus intraspecific phylogenomic origin affects preferential pairing and, therefore, the inheritance patterns. Despite its high level of heterozygosity, the important preferential chromosome pairing observed in sour orange results in a limited diversity of the genotypic variability of its diploid gametes, and consequently, a large part of the genetic value of the original diploid sour orange is transferred to the tetraploid progenies.

Integrated metabolomics and transcriptomics reveals difference involved in flavonoid and indole alkaloids biosynthesis in potato tuber flesh

Colored potatoes have garnered attention due to their higher nutrients compared to regular potatoes. This study describes a combined transcriptomic and metabolomic analysis of potato tubers originating from a single sexual cross between two parents with differing tuber skin and flesh colors. Through the use of RNA-seq, and UPLC-MS/MS metabolomics, this study aimed to elucidate the genetic and metabolic variations involved in the transmission of traits from tetraploid potato parents to hybrid F1 offspring. Our analysis revealed unique genes and metabolites associated with flavonoids and alkaloids within each group of offspring. Phenolic acids, flavonoids, and alkaloids are highlighted as key contributors to the positive heterosis observed in the tubers of potato hybrids, as assessed by calculating mid-parent heterosis for metabolites in three potato hybrids. At the overall metabolites level, hybrid SB (red-skinned and red-fleshed) exhibited a higher mid-parent heterosis than hybrid SA (purple-skinned and purple-fleshed) and SC (yellow-skinned and yellow-fleshed). Within hybrid SB tuber, specific accumulations of luteolin, salicin, isovitexin, and esculeoside B-5 were identified. Moreover, co-expression networks and correlation analysis pinpoint genes related to flavonoid and alkaloid biosynthesis. Notably, StDFR (dihydroflavonol reductase), a gene involved in flavonoid synthesis in potato tuber flesh, exhibits heightened expression in colored potato flesh. Additionally, we identified StYUCCA (indole-3-pyruvate monooxygenase), a gene regulating indole alkaloids synthesis, with elevated expression in yellow potato flesh. These findings provide insights into the utilization of heterosis breeding and the regulation of genes-metabolites in colored potato tuber flesh.

Elimination of Chromosomes as a Mechanism for the Formation of Diploid Plants in Diploid–Tetraploid Crosses in Maize (&lt;i&gt;Zea mays&lt;/i&gt; L.)

One of the main components of apomictic plant reproduction is the formation of unreduced embryo sacs (ESs). Heteroploid crosses, in which maternal diploid plants are pollinated by pollen of tetraploid paternal parent, can be used as an effective tool for identifying the ability to form unreduced ESs. In maize, in crosses 2n(♀) × 4n(♂), as a rule, shrunken kernels with a triploid embryo are formed, in which the development of the endosperm is impaired due to the deviation of the balance of the maternal (m) to paternal (p) genomes from the ratio of 2m : 1p. In our experiments, in several diploid maize lines, after their pollination with tetraploid pollen, the formation of large plump kernels was observed, from which diploid maternal-type plants developed, the maternal-type phenotype, as well as the hybrid endosperm phenotype, were confirmed by the expression of genetic markers. It has been suggested that the plump kernels in 2n × 4n crosses arise on the basis of unreduced embryo sacs (ESs) and pseudogamous apomixis, since the fusion of diploid sperms with diploid polar nuclei provides a 2 : 1 ratio of maternal to paternal genomes in the endosperm. In order to clarify the genetic nature of diploid plants phenotypically similar to maternal lines that developed from plump kernels in 2n × 4n crosses, we carried out their genotyping for all 10 chromosomes of the maize genome using polymorphic codominant SSR- and Indel-markers that differentiate the paternal line from maternal lines. As maternal lines, we used HPL AT, which has the ability to haploid parthenogenesis, KM, YuV-11, as well as the F2 B47/HPL AT hybrid plants; and as a paternal line – Chernaya Tetra(4n). It was found that in all the plants studied, when markers of five chromosomes (1, 2, 3, 4, and 9) were used, amplification of only maternal alleles was observed. However, in each of the studied plant, when using markers of other chromosomes, cases of amplification of alleles characteristic of the paternal line were noted. A hypothesis is put forward on the formation of diploid plants in 2n × 4n crosses in maize as a result of fertilization of the unreduced ESs and the subsequent elimination of chromosomes, predominantly of the pollen parent.

Triploid and aneuploid hybrids obtained from hybridization between Eriobotrya japonica and E. cavaleriei

A short ripening stage, multiple large seeds per fruit, and anthracnose disease seriously restrict the loquat (Eriobotrya japonica) industry. To obtain breeding germplasm of loquat with multiple ideal traits, a wild Eriobotrya species, E. cavaleriei (2n=2x=34), which flowers in late spring and early summer and whose fruits ripen in autumn, was used as the male parent to produce triploid plants from crosses with loquat tetraploid (2n=4x=68) lines (EjK474, EjB433 and EjB456). Fifteen progenies were obtained from three hybridizations, and 13 plants were identified as hybrids according to insertion-deletion (InDel) markers. All 13 hybrids were roughly identified as triploids by flow cytometry. Therein, 4 plants were identified as aneuploids with decreased or increased chromosome numbers based on sequencing depth according to reduced-representation genome sequencing. The sequencing depth on some chromosomes of these 4 hybrids was approximately 2/3 times or 1.41 times the average depth of all detected InDel loci. Frequencies of the loquat parent-specific alleles on increased or decreased chromosomes were approximately 50% or 75%. This verified that increased or decreased alleles in the 4 hybrids were all from tetraploid parents. The fruit flesh color genotypes of all hybrids were detected; there were two red-flesh alleles and one white-flesh allele in all hybrids. Leaves of E. cavaleriei were highly resistant to anthracnose in an in vitro assay, and the leaves of loquat B433 were sensitive. Disease spot diameters on the leaves of hybrids were significantly smaller (p < 0.01) than those of B433 after infection by spores of C. gloeosporioides. Therefore, the resistance of the hybrids was greater than that of the female parent B433. All these results showed that allotriploids can be obtained via hybridization between loquat tetraploids and E. cavaleriei, with some aneuploids as secondary products. Different flowering phases and fruit ripening stages, seedlessness and resistance to anthracnose might be combined in allotriploids. This study verified that resequencing can be used to identify the molecular karyotype of interspecific hybrids.

Global transcriptome analysis of allopolyploidization reveals large-scale repression of the D-subgenome in synthetic hexaploid wheat

Synthetic hexaploid wheat (SHW) lines are created as pre-breeding germplasm to diversify the D subgenome of hexaploid wheat and capitalize upon the untapped genetic diversity of the Aegilops tauschii gene pool. However, the phenotypes observed in the Ae. tauschii parents are not always recovered in the SHW lines, possibly due to inter-subgenome interactions. To elucidate this post-polyploidization genome reprogramming phenomenon, we performed RNA-seq of four SHW lines and their corresponding tetraploid and diploid parents, across ten tissues and three biological replicates. Homoeologue expression bias (HEB) analysis using more than 18,000 triads suggests massive suppression of homoeoalleles of the D subgenome in SHWs. Comparative transcriptome analysis of the whole-genome gene set further corroborated this finding. Alternative splicing analysis of the high-confidence genes indicates an additional layer of complexity where all five splice events are identified, and retained intron is predominant. Homoeologue expression upon resynthesis of hexaploid wheat has implications to the usage and handling of this germplasm in breeding as it relates to capturing the effects of epistatic interaction across subgenomes upon polyploidization. Special considerations must be given to this germplasm in pre-breeding activities to consider the extent of the inter-subgenome interactions on gene expression and their impact on traits for crop improvement.

Meiotic Behaviors of Allotetraploid Citrus Drive the Interspecific Recombination Landscape, the Genetic Structures, and Traits Inheritance in Tetrazyg Progenies Aiming to Select New Rootstocks.

Sexual breeding at the tetraploid level is a promising strategy for rootstock breeding in citrus. Due to the interspecific origin of most of the conventional diploid citrus rootstocks that produced the tetraploid germplasm, the optimization of this strategy requires better knowledge of the meiotic behavior of the tetraploid parents. This work used Genotyping By Sequencing (GBS) data from 103 tetraploid hybrids to study the meiotic behavior and generate a high-density recombination landscape for their tetraploid intergenic Swingle citrumelo and interspecific Volkamer lemon progenitors. A genetic association study was performed with root architecture traits. For citrumelo, high preferential chromosome pairing was revealed and led to an intermediate inheritance with a disomic tendency. Meiosis in Volkamer lemon was more complex than that of citrumelo, with mixed segregation patterns from disomy to tetrasomy. The preferential pairing resulted in low interspecific recombination levels and high interspecific heterozygosity transmission by the diploid gametes. This meiotic behavior affected the efficiency of Quantitative Trait Loci (QTL) detection. Nevertheless, it enabled a high transmission of disease and pest resistance candidate genes from P. trifoliata that are heterozygous in the citrumelo progenitor. The tetrazyg strategy, using doubled diploids of interspecific origin as parents, appears to be efficient in transferring the dominant traits selected at the parental level to the tetraploid progenies.

Crossability Relationship between Wild Cotton G. anomalum and G. aridum with Upland Cotton (G. hirsutum)

Background: Utilizing two wild cotton species, Gossypium anomalum [Wawra and Peyritsch (2n=2x=26) B1] and Gossypium aridum [Skovsted (2n=2x=26) D4], extensive wide hybridization event carried out with upland cotton to assess the feasibility and ease of delivering genetic variation responsible for resistance to various stresses. Methods: The crossing was carried out using the wild species and the cultivate varieties of upland cotton in 2021-2022 at TNAU, Coimbatore. Total of 12 crosses were attempted and the various aspect regarding the feasibility success of different crosses was studied. Result: In contrast to their reciprocals, viable offspring were generated in the direct crosses with tetraploid parents employed as seed parents with both wild species. A huge bulk of bolls dropped during the first seven days of pollination and no matured boll set was observed in reciprocals. Most G. anomalum hybrids produce F1 offspring with thick and long leaf hairs which help the plant attain resistance against sucking pests. Through successive backcrosses or chromosome duplication, such genetic material potentially can be utilized furthermore in plant breeding to provide new beneficial resistance traits apart from other significant and relevant features.

Comparative analysis of Fusarium crown rot resistance in synthetic hexaploid wheats and their parental genotypes

BackgroundFusarium crown rot (FCR) is a chronic disease of cereals worldwide. Compared with tetraploid wheat, hexaploid wheat is more resistant to FCR infection. The underlying reasons for the differences are still not clear. In this study, we compared FCR responses of 10 synthetic hexaploid wheats (SHWs) and their tetraploid and diploid parents. We then performed transcriptome analysis to uncover the molecular mechanism of FCR on these SHWs and their parents.ResultsWe observed higher levels of FCR resistance in the SHWs compared with their tetraploid parents. The transcriptome analysis suggested that multiple defense pathways responsive to FCR infection were upregulated in the SHWs. Notably, phenylalanine ammonia lyase (PAL) genes, involved in lignin and salicylic acid (SA) biosynthesis, exhibited a higher level of expression to FCR infection in the SHWs. Physiological and biochemical analysis validated that PAL activity and SA and lignin contents of the stem bases were higher in SHWs than in their tetraploid parents.ConclusionOverall, these findings imply that improved FCR resistance in SHWs compared with their tetraploid parents is probably related to higher levels of response on PAL-mediated lignin and SA biosynthesis pathways.

Haplotype variants of the stripe rust resistance gene Yr28 in Aegilops tauschii.

Stripe rust resistance gene YrAet672 from Aegilops tauschii accession CPI110672 encodes a nucleotide-binding and leucine-rich repeat domain containing protein similar to YrAS2388 and both these members were haplotypes of Yr28. New sources of host resistance are required to counter the continued emergence of new pathotypes of the wheat stripe rust pathogen Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst). Here, we show that CPI110672, an Aegilops tauschii accession from Turkmenistan, carries a single Pst resistance gene, YrAet672, that is effective against multiple Pst pathotypes, including the four predominant Pst lineages present in Australia. The YRAet672 locus was fine mapped to the short arm of chromosome 4D, and a nucleotide-binding and leucine-rich repeat gene was identified at the locus. A transgene encoding the YrAet672 genomic sequence, but lacking a copy of a duplicated sequence present in the 3' UTR, was transformed into wheat cultivar Fielder and Avocet S. This transgene conferred a weak resistance response, suggesting that the duplicated 3' UTR region was essential for function. Subsequent analyses demonstrated that YrAet672 is the same as two other Pst resistance genes described in Ae. tauschii, namely YrAS2388 and Yr28. They were identified as haplotypes encoding identical protein sequences but are polymorphic in non-translated regions of the gene. Suppression of resistance conferred by YrAet672 and Yr28 in synthetic hexaploid wheat lines (AABBDD) involving Langdon (AABB) as the tetraploid parent was associated with a reduction in transcript accumulation.

Registration of six synthetic hexaploid wheat germplasm as sources of resistance to tan spot, stem rust, and stripe rust and adult plant resistance to leaf rust

AbstractAegilops tauschii is the donor of D‐genome of bread wheat (Triticum aestivum L.) as well as several agronomically desirable genes important for wheat improvement. The genetic transfers from Ae. tauschii to bread wheat are achieved either through direct crosses or indirectly through production of synthetic hexaploid wheat (SHW). Synthetic hexaploid wheat is produced by crossing tetraploid wheat (Triticum turgidum L.) with Ae. tauschii, followed by chromosome doubling of the F1 hybrid by colchicine. Six Ae. tauschii accessions based on their seedling resistance to tan spot, stem rust, stripe rust and adult plant resistance to leaf rust and two tetraploid wheat genotypes (tetraPrelude and tetraThatcher) were used for the production of SHWs. The present report describes the production and evaluation of six new SHWs, TA4161‐L1 (Reg. no. GP‐1071, PI 700779), TA4161‐L2 (Reg. no. GP‐1072, PI 700780), TA4161‐L3 (Reg. no. GP‐1073, PI 700781), TA4161‐L4 (Reg. no. GP‐1074, PI 700782), TA4161‐L5 (Reg. no. GP‐1075, PI 700783), and TA4161‐L6 (Reg. no. GP‐1076, PI 700784), for seedling resistance to tan spot, stem rest, stripe rust, and adult plant resistance to leaf rust. The SHWs reported here with higher levels of resistance to race 1 of Pyrenospora tritici‐repentis would be an excellent addition to the current collection of tan spot–resistant germplasm. The resistance to the three rusts was not expressed in the SHWs due to the presence of rust‐suppressor factors in tetraploid parents. However, the SHWs will be good source material for new resistance genes to the three rusts in derivative lines upon breeding with nonsuppressive wheat genotypes as well as for the mapping of rust‐suppressive factors.

Marker-assisted transfer of leaf and stripe rust resistance from Triticum turgidum var. durum cv. Trinakria to wheat variety HD2932.

A marker-assisted backcrossing program initiated to transfer leaf rust resistance gene LrTrk from Triticum turgidum cv. Trinakria to hexaploid wheat variety HD2932 cotransferred a stripe rust resistance gene, YrTrk, along with LrTrk. The cross of hexaploid recurrent parent HD2932 with tetraploid donor parent Trinakria produced pentaploid F1 plants. F1s were backcrossed with recurrent parent HD2932 to produce BC1F1 generation. Foreground and background selection was conducted in each backcross generation to identify plants for backcrossing or selfing. While foreground selection for LrTrk was carried out with linked and validated molecular marker Xgwm234, for background selection, 86 polymorphic SSR markers from the A and B genomes were used. Single selected plants from BC1F1 and BC2F1 generations backcrossed and selfed to produce BC2F1and BC2F2 generations, respectively. Background selection resulted in 83.72%, 91.86%, and 98.25% of RPG recovery in BC1F1, BC2F1, and BC2F2 generations, respectively. A total of 27 plants with LrTrk in homozygous state were identified in BC2F2 generation and selfed to produce 27 BC2F3 NILs. All the NILs were tested for leaf and stripe rust resistance at the seedling stage using seven Puccinia triticina and one Puccinia striiformis f.sp. tritici rust pathotypes. All the 27 NILs were found to be resistant to both leaf and stripe rust pathotypes. So, these NILs are designated to carry leaf and stripe rust resistance genes LrTrk/YrTrk.

Near-Hexaploid and Near-Tetraploid Aneuploid Progenies Derived from Backcrossing Tetraploid Parents Hibiscus syriacus × (H. syriacus × H. paramutabilis).

Hibiscus syriacus, azalea, is an important woody ornamental shrub planted throughout many temperate and subtropical regions of the world. However, flower size is smaller in this species than some of its relatives. To increase flower size, interspecific hybridization has been used, and such hybrid cultivars are usually characterized by larger flowers, increased vigor, diverse leaf shapes, and reduced fertility. Our earlier studies have shown that these hybrid cultivars could backcross with H. syriacus when used as male parents. To understand the breeding potential of these hybrid cultivars, two popular tetraploid hybrid cultivars, ‘Lohengrin’ and ‘Resi’, were used as pollen parents to backcross several tetraploid H. syriacus cultivars. As a result, 28.76% and 64.4% of ‘Lohengrin’ and ‘Resi’ progenies exhibited larger flowers than both of their parents. Interestingly, 14 of 18 progenies of ‘Resi’ were putative hexaploids, whereas 19 tested ‘Lohengrin’ progenies were tetraploid. Because putative hexaploid progenies were only observed among progenies of ‘Resi’, this hybrid cultivar appears to produce unreduced gametes. In addition, among the 14 putative hexaploids derived from ‘Resi’, 11 had larger flowers than both of their parents and their tetraploid siblings (p < 0.05). The 45S rDNA and 5S rDNA locus segregation among those BC1F1 progenies was tested by fluorescent in situ hybridization (FISH), and the wide range of 45S rDNA signal numbers among siblings indicated that these aneuploids resulted from unequal segregation or chromosome rearrangement. Chromosome counting confirmed aneuploidy among BC1F1 progenies. Ploidy diversity and aneuploidy have been known to contribute to various elements of morphological diversity, such as larger flower size and reduced fertility, which are important in ornamental plant breeding. The present study demonstrated the breeding potential of interspecific Hibiscus cultivars for increasing ploidy level and flower size.

The growth, survival and ploidy of diploid, triploid and tetraploid of the Pacific oyster (Crassostrea gigas) in larval and juvenile stages

Slow growth and genomic instability are the main problems facing tetraploid oyster breeding. In response to the above problem, we developed tetraploid by using Crassostrea gigas ‘Haida No.3’, a new variety with rapid growth and black shell color, and analyzed the growth, survival and ploidy of diploid ♀ × diploid ♂ (DD), diploid ♀ × tetraploid ♂ (DT: triploid) and tetraploid ♀ × tetraploid ♂(TT) in different periods. The results showed that there was no significant difference between the fertilization rate of DD, DT and TT, but the hatching rate of TT was significantly lower than that of DD (P < 0.05). The shell height of TT was significantly lower than DD, and the shell height of DT was significantly higher than that of DD at 13 days (P < 0.05). The survival rate of TT was lower than that of DD and DT in larval stage (P < 0.05), while there was no significant difference in the mean survival rate of DD, DT and TT in juvenile stage. The tetraploid rate in TT was 100% during the larval and juvenile stages. The shell color of all progeny in TT and DT was black and consistent with C. gigas ‘Haida No.3’. These results indicated that black shell color of C. gigas ‘Haida No.3’ could be stably passed on to triploid and tetraploid offspring, suggesting that establishing genomically stable tetraploid populations was feasible by screening tetraploid parents.

Biofortified wheat: Harnessing genetic diversity for improved nutritional quality to eradicate hidden hunger

AbstractThe present study is based on backcross introgression lines carrying high grain zinc (Zn) quantitative trait loci (QTL) introgressed from domestic einkorn wheat (Triticum monococcum L.) and wild einkorn wheat (T. boeoticum) in the background of high‐yielding wheat (T. aestivum L.) cultivars of India. Initially, individual trials each for BC1F3 and BC2F3 progenies from different cross combinations were evaluated for grain Zn concentration, yellow pigment content (YPC) and agronomic traits. Highly promising BC1F3 and BC2F3 progenies were identified and advanced in off‐season as ear to progeny rows. A total of 42 BC1F5 and 43 BC2F5 derivatives were evaluated in a single trial where the BC1F5 progenies from recipient parent WH1105 and tetraploid parent Donor 2 were recorded with highest grain Zn (64.1–67.9 ppm) showing up to 35.8% enhancement over recipient. The highest grain YPC (5.35 ppm) was observed for BC1F5 progenies from the cross involving PBW703 (3.34 ppm) as recipient and Donor 7 (6.32 ppm) as tetraploid donor parent. Monitoring of backcross derivatives with the marker YP7A‐2 linked to yellow pigment gene Psy‐A1, also revealed nine lines positive for high yellow pigment allele (Psy‐A1c) indicating introgression from durum wheat (T. durum Desf.). Nineteen high Zn derivatives were shortlisted and selfed for 2 yr (2017–2018 and 2018–2019) to get desirable homozygosity and preliminary yield evaluation was conducted for two consecutive years (2019–2020 and 2020–2021). Introgression lines in the background of PBW698 (IL8 and IL17) were recorded with the highest Zn concentration (51.37 and 51.30 ppm) indicating 55.90% increment over recipient parent with good agronomic performance. These biofortified introgression wheat lines can contribute to mitigating the malnutrition among the masses in developing countries.

Nonadditive gene expression is correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow (Salix spp.).

Many studies have highlighted the complex and diverse basis for heterosis in inbred crops. Despite the lack of a consensus model, it is vital that we turn our attention to understanding heterosis in undomesticated, heterozygous, and polyploid species, such as willow (Salix spp.). Shrub willow is a dedicated energy crop bred to be fast-growing and high yielding on marginal land without competing with food crops. A trend in willow breeding is the consistent pattern of heterosis in triploids produced from crosses between diploid and tetraploid species. Here, we test whether differentially expressed genes are associated with heterosis in triploid families derived from diploid Salix purpurea, diploid Salix viminalis, and tetraploid Salix miyabeana parents. Three biological replicates of shoot tips from all family progeny and parents were collected after 12 weeks in the greenhouse and RNA extracted for RNA-Seq analysis. This study provides evidence that nonadditive patterns of gene expression are correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow. Expression-level dominance was most correlated with heterosis for biomass yield traits and was highly enriched for processes involved in starch and sucrose metabolism. In addition, there was a global dosage effect of parent alleles in triploid hybrids, with expression proportional to copy number variation. Importantly, differentially expressed genes between family parents were most predictive of heterosis for both field and greenhouse collected traits. Altogether, these data will be used to progress models of heterosis to complement the growing genomic resources available for the improvement of heterozygous perennial bioenergy crops.

Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization.

BackgroundHawthorn species (Crataegus L.; Rosaceae tribe Maleae) form a well-defined clade comprising five subgeneric groups readily distinguished using either molecular or morphological data. While multiple subsidiary groups (taxonomic sections, series) are recognized within some subgenera, the number of and relationships among species in these groups are subject to disagreement. Gametophytic apomixis and polyploidy are prevalent in the genus, and disagreement concerns whether and how apomictic genotypes should be recognized taxonomically. Recent studies suggest that many polyploids arise from hybridization between members of different infrageneric groups.MethodsWe used target capture and high throughput sequencing to obtain nucleotide sequences for 257 nuclear loci and nearly complete chloroplast genomes from a sample of hawthorns representing all five currently recognized subgenera. Our sample is structured to include two examples of intersubgeneric hybrids and their putative diploid and tetraploid parents. We queried the alignment of nuclear loci directly for evidence of hybridization, and compared individual gene trees with each other, and with both the maximum likelihood plastome tree and the nuclear concatenated and multilocus coalescent-based trees. Tree comparisons provided a promising, if challenging (because of the number of comparisons involved) method for visualizing variation in tree topology. We found it useful to deploy comparisons based not only on tree-tree distances but also on a metric of tree-tree concordance that uses extrinsic information about the relatedness of the terminals in comparing tree topologies.ResultsWe obtained well-supported phylogenies from plastome sequences and from a minimum of 244 low copy-number nuclear loci. These are consistent with a previous morphology-based subgeneric classification of the genus. Despite the high heterogeneity of individual gene trees, we corroborate earlier evidence for the importance of hybridization in the evolution of Crataegus. Hybridization between subgenus Americanae and subgenus Sanguineae was documented for the origin of Sanguineae tetraploids, but not for a tetraploid Americanae species. This is also the first application of target capture probes designed with apple genome sequence. We successfully assembled 95% of 257 loci in Crataegus, indicating their potential utility across the genera of the apple tribe.

QTL mapping in outbred tetraploid (and diploid) diallel populations.

Over the last decade, multiparental populations have become a mainstay of genetics research in diploid species. Our goal was to extend this paradigm to autotetraploids by developing software for quantitative trait locus (QTL) mapping in connected F1 populations derived from a set of shared parents. For QTL discovery, phenotypes are regressed on the dosage of parental haplotypes to estimate additive effects. Statistical properties of the model were explored by simulating half-diallel diploid and tetraploid populations with different population sizes and numbers of parents. Across scenarios, the number of progeny per parental haplotype (pph) largely determined the statistical power for QTL detection and accuracy of the estimated haplotype effects. Multiallelic QTL with heritability 0.2 were detected with 90% probability at 25 pph and genome-wide significance level 0.05, and the additive haplotype effects were estimated with over 90% accuracy. Following QTL discovery, the software enables a comparison of models with multiple QTL and nonadditive effects. To illustrate, we analyzed potato tuber shape in a half-diallel population with three tetraploid parents. A well-known QTL on chromosome 10 was detected, for which the inclusion of digenic dominance lowered the Deviance Information Criterion (DIC) by 17 points compared to the additive model. The final model also contained a minor QTL on chromosome 1, but higher-order dominance and epistatic effects were excluded based on the DIC. In terms of practical impacts, the software is already being used to select offspring based on the effect and dosage of particular haplotypes in breeding programs.