The timing of flowering during the year is an important adaptive character affecting reproductive success in plants and is critical to crop yield. Flowering time has been extensively manipulated in crops such as wheat ( Triticum aestivum L.) during domestication, and this enables them to grow productively in a wide range of environments. Several major genes controlling flowering time have been identified in wheat with mutant alleles having sequence changes such as insertions, deletions or point mutations. We investigated genetic variants in commercial varieties of wheat that regulate flowering by altering photoperiod response ( Ppd-B1 alleles) or vernalization requirement ( Vrn-A1 alleles) and for which no candidate mutation was found within the gene sequence. Genetic and genomic approaches showed that in both cases alleles conferring altered flowering time had an increased copy number of the gene and altered gene expression. Alleles with an increased copy number of Ppd-B1 confer an early flowering day neutral phenotype and have arisen independently at least twice. Plants with an increased copy number of Vrn-A1 have an increased requirement for vernalization so that longer periods of cold are required to potentiate flowering. The results suggest that copy number variation (CNV) plays a significant role in wheat adaptation.

HighlightThe major flowering time genes cloned to date regulate photoperiod and vernalization response. We identified a deletion containing genes regulating earliness per se, which fine tune flowering in hexaploid wheat.

Vernalization, photoperiod and the relatively poorly defined earliness per se (eps) genes regulate flowering in plants. We report here the validation of a major eps quantitative trait locus (QTL) located on wheat 1DL using near isogenic lines (NILs). We used four independent pairs of NILs derived from a cross between Spark and Rialto winter wheat varieties, grown in both the field and controlled environments. NILs carrying the Spark allele, defined by QTL flanking markers Xgdm111 and Xbarc62, consistently flowered 3–5 days earlier when fully vernalized relative to those with the Rialto. The effect was independent of photoperiod under field conditions, short days (10-h light), long days (16-h light) and very long days (20-h light). These results validate our original QTL identified using doubled haploid (DH) populations. This QTL represents variation maintained in elite north-western European winter wheat germplasm. The two DH lines used to develop the NILs, SR9 and SR23 enabled us to define the location of the 1DL QTL downstream of marker Xgdm111. SR9 has the Spark 1DL arm while SR23 has a recombinant 1DL arm with the Spark allele from Xgdm111 to the distal end. Our work suggests that marker assisted selection of eps effects is feasible and useful even before the genes are cloned. This means eps genes can be defined and positionally cloned in the same way as the photoperiod and vernalization genes have been. This validation study is a first step towards fine mapping and eventually cloning the gene directly in hexaploid wheat.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-014-0094-3) contains supplementary material, which is available to authorized users.

Differences in time to heading that remain after photoperiod and vernalisation requirements have been saturated are classified as earliness per se ( Eps ) effects. It has been commonly assumed that Eps genes are purely constitutive and independent of environment, although the likely effect of temperature on Eps effects in hexaploid wheat has never been tested. We grew four near isogenic lines (NILs) for the Eps gene located in chromosome 1D ( Eps-D1 ) at 6, 9, 12, 15, 18, 21 and 24 °C. In line with expectations we found that lines carrying the Eps -late allele were always later than those with Eps -early alleles. But in addition, we reported for the first time that the magnitude of the effect increased with decreasing temperature: an Eps x temperature interaction in hexaploid wheat. Variation in heading time due to Eps x temperature was associated with an increase in sensitivity to temperature mainly during late reproductive phase. Moreover, we showed that Eps alleles exhibited differences in cardinal (base, optimum, maximum) temperatures and that the expression of ELF3 , (the likely candidate for Eps-D1 ) also interacted with temperature.

Identification of earliness per se (Eps) flowering time loci in spring wheat are troublesome due to confounding effects of vernalization and photoperiod responses. The Wheat Association Mapping Initiative panel of 287 elite lines was assessed to identify genomic regions associated with Eps and to understand the effects of vernalization and photoperiod treatments in spring wheat. The panel was grown under field conditions with four different treatments: (i) vernalization, where 1-d germinated seeds were kept at 4°C for 6 to 8 wk; (ii) extended photoperiod treatment, from seedling emergence to 10 d after anthesis in the field; (iii) treatments (i) and (ii) in combination; and (iv) a control treatment without either (i) or (ii). The combined vernalization and photoperiod treatments had the greatest effect in advancing the flowering time (4 d). Genome-wide association study in this panel on treatment (iii) detected a locus for Eps in chromosome 1D at 163 to 167 cM. An analysis of the flowering time data on this panel from 19 international environments did not show the presence of Eps in chromosome 1D, indicating the possible masking effect of vernalization and photoperiod genes. This study also validated the diagnostic marker-a transcription factor in the circadian clock input pathway called Triticum aestivum EARLY FLOWERING 3-that is associated with Eps in chromosome 1D and can be used for marker-assisted selection.

Perception of photoperiod changes enables plants to flower under optimum conditions for survival. We used doubled haploid populations of crosses among Avalon × Cadenza, Charger × Badger and Spark × Rialto and identified short‐day flowering time response quantitative trait loci (QTL) on wheat chromosomes 1BS and 1BL. We used synteny between Brachypodium distachyon and wheat to identify potential candidates for both QTL. The 1BL QTL peak coincided with TaFT3‐B1, a homologue of the barley gene HvFT3, the most likely candidate gene. The 1BS QTL peak coincided with homologues of Arabidopsis thaliana S ENSITIVITY TO R ED LIGHT R EDUCED 1, WUSCHEL‐like and RAP2.7, which is also known as Zea mays TARGET OF EAT1, named TaSRR1‐B1, TaWUSCHELL‐B1 and TaTOE1‐B1, respectively. Gene expression assays suggest that TaTOE1‐B1 and TaFT3‐B1 are expressed more during short days. We identified four alleles of TaFT3‐B1 and three alleles of TaTOE1‐B1. We studied the effect of these alleles in the Watkins and GEDIFLUX diversity panels by using 936 and 431 accessions, respectively. Loss of TaFT3‐B1 by deletion was associated with late flowering. Increased TaFT3‐B1 copy number was associated with early flowering, suggesting that TaFT3‐B1 promotes flowering. Significant association was observed in the GEDIFLUX collection for TaTOE1‐B1, a putative flowering repressor.

Photoperiod (day-length) response, vernalization (response to extended periods of cold) and earliness per se ( Eps ) genes regulate fl owering time in wheat. The vernalization and photoperiod response genes are relatively well studied. However, the role of Eps genes is yet to be fully understood but the current assumption is that Eps genes regulate fl owering independent of vernalization and photoperiod. While some Eps genes have been cloned in both Hordeum vulgare and Triticum monococcum , none has been cloned in Triticum aestivum to date. The use of near isogenic lines (NILs) in both T. monococcum and Triticum aestivum has enabled Eps effects to be studied in more detail and candidate genes have been proposed for Eps effects in both species. Eps loci are reported to be involved in fi ne tuning fl owering time and are also responsible for controlling spikelet number and size hence could be manipulated to increase wheat yield. This mini review summarises our current understanding of Eps and how manipulation of Eps genes can be used in predictive wheat breeding.The world population demands more food, greater diversity of food, a balanced and healthy diet, produced on no more, and preferably less land, while conserving soil, water, and genetic resources. The major problem is that even though wheat yields are increasing (Lopes et al. 2012 ), the percentage increase is below the projected percentage demand with about 0.6 % defi cit projected annually until 2050 (Dixon et al. 2009 ;Rosegrant and Agcaoili 2010 ). The challenge wheat breeders face is to bridge the gap between wheat demand and wheat production. It is therefore vital to direct wheat breeding efforts to the production of higher yielding varieties in order to ensure current and future food security (Reyolds et al. 2012 ). The part of the wheat plant that is important for direct consumption by humans is the grain and its production is dependent on fl owering time. Manipulating fl owering time is one avenue that can be exploited to increase wheat grain yield (Herndl et al. 2008 ; Greenup et al. 2009 ). However, in order to successfully increase grain yield, it is

Abstract. Makore F, Gasura E, Souta C, Mazamura U, Derera J, Zikhali M, Kamutando CN, Magorokosho C, Dari S. 2021. Molecular characterization of a farmer-preferred maize landrace population from a multiple-stress-prone subtropical lowland environment. Biodiversitas 22: 769-777.  The study was conducted to assess genetic diversity of 372 maize lines using 116 single nucleotide polymorphism (SNP) markers. Three hundred and forty-seven lines were S1 lines (coded J lines) from a local maize landrace population and twenty-five were the widely used standard lines. The number of alleles per marker ranged from two to four and the average was three alleles.  The average polymorphic information content (PIC) value of 0.405 indicates high genetic diversity for maize lines evaluated in this study. Population structure revealed three distinct sub-populations. Sub-population 1 contained two J lines; sub-population 2 contained five J lines and sub-population 3 contained the rest of the J lines and all the standard lines. Analysis of molecular variance (AMOVA) identified 22% variance among and 78% variance within the three subpopulations, indicating high gene exchange and low genetic differentiation. Hierarchical cluster analysis further divided the lines into nine subgroups placing some of the J lines into known heterotic groups', i.e.,  J30_3, J393_4, J393_3, and J393_1 in CIMMYT heterotic group B. Allelic variation observed can be a source of allele combination for breeding programs interested in widening their genetic base. The private alleles that were present in the J lines suggest availability of stress-tolerant genes that breeders can incorporate in new hybrids.