Wild relatives for crop breeding: potential of nuclear variability in Hordeum chilense Roem. et Schultz

The progressive narrowing of the genetic base in crops (Tanksley and McCouch, Reference Tanksley and McCouch1997; Warburton et al., Reference Warburton, Crossa, Franco, Kazi, Trethowan, Rajaram, Pfeiffer, Zhang, Dreisigacker and Ginkel2006) has promoted a renewed interest in wild relatives such as Hordeum vulgare ssp. spontaneum (Matus et al., Reference Matus, Corey, Filichkin, Hayes, Vales, Kling, Riera-Lizarazu, Sato, Powell and Waugh2003; Inostroza et al., Reference Inostroza, del Pozo, Matus, Castillo, Hayes, Machado and Corey2009) or other distant relatives such as Aegilops tauschii, donor of the D genome of common wheat (van Ginkel and Ogbonnaya, Reference van Ginkel and Ogbonnaya2007); or H. chilense Roem. et Schultz. (Atienza et al., Reference Atienza, Gimenez, Martin and Martin2000; Atienza et al., Reference Atienza, Satovic, Martin and Martin2005b; Martin et al., Reference Martin, Atienza, Ramirez, Barro and Martin2008b). The wild barley H. chilense shows a wide range of variation (at both morphological and molecular levels) distributed into two main groups plus an intermediate group, as revealed by molecular markers (Vaz Patto et al., Reference Vaz Patto, Aardse, Buntjer, Rubiales, Martin and Niks2001; Castillo et al., Reference Castillo, Budak, Martin, Dorado, Borner, Roder and Hernandez2010). The high compatibility of H. chilense with the genomes of Triticum species gives rise to fertile and stable amphiploids and allows the transfer of traits to wheat (Martin et al., Reference Martin, Martín, Cabrera, Ramírez, Giménez, Rubiales, Hernández, Ballesteros and Jaradat1998), such as resistance to septoria tritici, abiotic stress tolerance or endosperm storage proteins (Martin et al., Reference Martin, Alvarez, Martin, Barro and Ballesteros1999; Atienza et al., Reference Atienza, Alvarez, Villegas, Gimenez, Ramirez, Martin and Martin2002), but probably the main interest of this species is its potential for increasing carotenoid content (Alvarez et al., Reference Alvarez, Martin and Martin1999; Atienza et al., Reference Atienza, Ramirez, Hernandez and Martin2004; Atienza et al., Reference Atienza, Avila, Ramirez and Martin2005a; Atienza et al., Reference Atienza, Ballesteros, Martin and Hornero-Mendez2007b). The phytoene synthase 1 from H. chilense is a good candidate gene for the improvement of carotenoid content (Atienza et al., Reference Atienza, Avila and Martin2007a), and, therefore, the cloning and characterization of this gene offer new possibilities for wheat breeding (Rodriguez-Suarez et al., Reference Rodriguez-Suarez, Gimenez and Atienza2010). Similarly, the development of H. chilense durum wheat chromosome substitution lines will be useful for evaluating the substitution effect of durum wheat by H. chilense genes for carotenoid content. The use of barley expressed sequence tag (EST) markers (Hagras et al., Reference Hagras, Kishii, Sato, Tanaka and Tsujimoto2005a; Hagras et al., Reference Hagras, Kishii, Tanaka, Sato and Tsujimoto2005b; Nasuda et al., Reference Nasuda, Kikkawa, Ashida, Rafiqul Islam, Sato and Endo2005) has proven very useful for physical mapping in H. chilense (Atienza et al., Reference Atienza, Martin and Martin2007c; Said and Cabrera, Reference Said and Cabrera2009; Cherif-Mouaki et al., Reference Cherif-Mouaki, Said, Alvarez and Cabrera2011). Besides, the development of the genetic linkage map using ESTs, conserved orthologous set (Bolot et al., Reference Bolot, Abrouk, Masood-Quraishi, Stein, Messing, Feuillet and Salse2009) and H. chilense-specific diversity arrays technology markers will allow the establishment of precise relationships between H. chilense and related species genomes, thus providing more efficient tools for the use of this wild barley in wheat breeding.

Cytoplasm×nuclear variability in H. chilense–wheat interactions

The nuclear genome has a predominating role for the inheritance of most plant traits Nevertheless, cytoplasmic factors and cytoplasm × nucleus interactions are also important and still largely unexplored. Genetic information of eukaryotic organisms is divided into a nuclear genome in the nucleus and organelle genomes (sometimes referred to as plasmon) in the cytoplasm. Since the cytoplasm is maternally inherited in Triticeae species (Kihara, Reference Kihara1951), the best way to investigate nuclear–cytoplasm interactions is by developing alloplasmic lines, i.e. lines with the same nucleus but cytoplasms from different species.

H. chilense–wheat alloplasmic lines have been developed by repeated substitution backcross as described by Kihara (Reference Kihara1951). First, amphiploids H. chilense × wheat are developed as described by Martin and Chapman (Reference Martin and Chapman1977). This step is essential since the hybrids between H. chilense and wheat are sterile while the amphiploids are fertile. Backcrossing to the nucleus donor is repeated until H. chilense chromosomes are fully eliminated. After somatic chromosome counting, the cytoplasm origin has to be checked, since paternal inheritance of cytoplasm has also been reported (Soliman et al., Reference Soliman, Fedak and Allard1987; Laser et al., Reference Laser, Mohr, Odenbach, Oettler and Kück1997; Aksyonova et al., Reference Aksyonova, Sinyavskaya, Danilenko, Pershina, Nakamura and Davydenko2005; Badaeva et al., Reference Badaeva, Pershina and Bildanova2006). Indeed, we have observed this phenomenon with both H. chilense (Atienza et al., Reference Atienza, Martin, Ramirez, Martin and Ballesteros2007d) and H. vulgare cytoplasms (Martin et al., Reference Martin, Atienza and Barro2008a) using the chloroplastic marker ccSSR4 (Chung and Staub, Reference Chung and Staub2003).

Alloplasmic lines are very useful for elucidating plant phylogeny and determining the genetic effect of different plasmons. Furthermore, since the discovery of cytoplasmic male sterility (CMS) in wheat (Kihara, Reference Kihara1951), breeders have been very interested in CMS systems, looking for a viable procedure for hybrid wheat production (for a review, see Martin, Reference Martin2009).

The development of H. chilense–common wheat alloplasmic lines gives rise to two types of lines: male-sterile when the line H1 is used as cytoplasm donor, or fully fertile when other H. chilense lines are used. Accordingly, a research line is being developed to investigate the potential of this new CMS source, designated msH1, to produce hybrid wheat. The male sterile line does not show any floral or developmental abnormalities, but reduced height and delayed heading (Martin et al., Reference Martin, Atienza, Ramirez, Barro and Martin2008b). Fertility restoration is obtained when chromosome 6H^chS from H. chilense line H1 is added (Martin et al., Reference Martin, Atienza, Ramirez, Barro and Martin2008b). Further research allowed the obtaining of a fertile euplasmic line carrying the translocation T6HchS·6DL (Martin et al., Reference Martin, Atienza, Ramirez, Barro and Martin2009). However, a single dose of this translocation is insufficient for fertility restoration, which suggests the presence of one or more inhibitors of fertility genes in chromosome 6DL (Martin et al., Reference Martin, Atienza, Ramirez, Barro and Martin2009). More recently, a highly fertile line with 42 chromosomes plus an extra acrocentric chromosome has been obtained (Martin et al., Reference Martin, Atienza, Ramírez, Barro and Martin2010), whose long arm is the 1H^chS chromosome, as demonstrated by molecular markers and fluorescent in situ hybridization. It seems that this chromosome originated from a deletion of the distal part of chromosome 1H^chL and that the restorer gene is located on the retained segment from the 1H^chL (Martin et al., Reference Martin, Atienza, Ramírez, Barro and Martin2010). The disomic addition of this acrocentric chromosome is fully fertile and thus constitutes an additional source of restoration for wheat hybrid production based on msH1 system.

On the other hand, fully fertile alloplasmic lines were also obtained (Atienza et al., Reference Atienza, Martin, Ramirez, Martin and Ballesteros2007d). Preliminary evidence suggested that phenotypic and metabolic variations in wheat are associated with different nuclear–cytoplasmic combinations (Atienza et al., Reference Atienza, Martin and Martin2007c; Atienza et al., Reference Atienza, Martín, Pecchioni, Platani and Cattivelli2008), including phenotypic traits such as height or quality traits like endosperm carotenoid content. In other cases, the use of either wheat or H. chilense cytoplasm did not result in any phenotypic variation in Tritordeum (Atienza et al., Reference Atienza, Ramirez, Martin and Ballesteros2007e). The genetic effects of the plasmon have been studied in several species affecting different traits including yield (Loessl et al., Reference Loessl, Goetz, Braun and Wenzel2000), disease or pest resistance (Voluevich and Buloichik, Reference Voluevich and Buloichik1992; Matsui et al., Reference Matsui, Yoshida, Ban, Komatsuda and Kawada2002) and tolerance to abiotic stresses (Uprety and Tomar, Reference Uprety and Tomar1993; Shonnard and Gepts, Reference Shonnard and Gepts1994; Zhang et al., Reference Zhang, Yu and Zhang2003). Nevertheless, the most detailed studies have been performed in the Triticum–Aegilops complex (Tsunewaki et al., Reference Tsunewaki, Wang and Matsuoka1996, Reference Tsunewaki, Wang and Matsuoka2002; Tsunewaki, Reference Tsunewaki2009) and in teosinte–maize combinations (Allen, Reference Allen2005).

Recently, parallel transcriptomic and metabolomic analyses have been carried out on three alloplasmic lines to investigate the effect of H. chilense, Ae. uniaristata and Ae. squarrosa cytoplasms on nuclear–cytoplasm interaction with common wheat (Crosatti et al., Reference Crosatti, Quansah, Atienza, Mare, Fait and Cattivelli2010). The gas chromatography-mass spectrometer metabolic profiling of leaves revealed significant differences between the alloplasmic lines and their euplasmic control. Transcriptomic analyses using the Affimetrix 61k wheat gene chip showed that more than 500 genes modified their behaviour in the H. chilense alloplasmic line compared with the euplasmic control (Crosatti et al., Reference Crosatti, Quansah, Atienza, Mare, Fait and Cattivelli2010). Most of them encoded for chloroplast/mitochondrion localized proteins. The simultaneous consideration of transcriptomic and metabolomic data underlined that the amino-acid biosynthetic pathways are highly dependent on the nuclear–cytoplasm interaction.

In conclusion, H. chilense is an interesting source of variability for wheat breeding and the study of the alloplasmic lines allows us to increase our understanding of how nuclear and cytoplasmic genomes interact. Thus, this may open up new opportunities for plant improvement through cytoplasm modification.