Crop breeding for salt tolerance in the era of molecular markers and marker‐assisted selection

Crop salt tolerance (ST) is a complex trait affected by numerous genetic and non‐genetic factors, and its improvement via conventional breeding has been slow. Recent advancements in biotechnology have led to the development of more efficient selection tools to substitute phenotype‐based selection systems. Molecular markers associated with genes or quantitative trait loci (QTLs) affecting important traits are identified, which could be used as indirect selection criteria to improve breeding efficiency via marker‐assisted selection (MAS). While the use of MAS for manipulating simple traits has been streamlined in many plant breeding programmes, MAS for improving complex traits seems to be at infancy stage. Numerous QTLs have been reported for ST in different crop species; however, few commercial cultivars or breeding lines with improved ST have been developed via MAS. We review genes and QTLs identified with positive effects on ST in different plant species and discuss the prospects for developing crop ST via MAS. With the current advances in marker technology and a better handling of genotype by environment interaction effects, the utility of MAS for breeding for ST will gain momentum.     

Introducing host‐plant resistance to anthracnose in Kyrgyz common bean through inoculation‐based and marker‐aided selection

Common bean (Phaseolus vulgaris L.) is one of the most important legume crops for human consumption. However, its grain yield can be reduced by up to 90% by the seedborne disease, anthracnose. Fungicide treatment is costly and time‐consuming. The introduction of host plant resistance against this disease appears, therefore, to be crucial for enhancing the productivity of this crop in Kyrgyzstan. The use of DNA‐based markers in backcrossing programmes may help speed up the breeding for resistance. In this study, we used a combination of inoculation tests and a DNA marker (SCAreoli marker) to track the transfer of host‐plant resistance (Co‐2 gene) from two donor cultivars, ‘Vaillant’ and ‘Flagrano’, to susceptible Kyrgyz cultivars ‘Ryabaya’, ‘Kytayanka’ and ‘Lopatka’, which are widely grown in the country. The segregating offspring were evaluated to test the reliability of the SCAreoli marker as selection aid for host‐plant resistance to anthracnose. Our study showed that a co‐dominant DNA marker can successfully be used in backcross breeding to distinguish segregating material in different market classes of common bean.     

Introgression of clubroot resistance into an elite pak choi inbred line through marker‐assisted introgression breeding

Clubroot is a soilborne disease that severely infects cruciferous species. Pak choi (Brassica rapa subsp. chinensis) is an economically important cruciferous crop cultivated throughout the world. However, no clubroot‐resistant germplasms have been identified in pak choi to date. To improve disease resistance, we used marker‐assisted selection (MAS) to introgress the clubroot resistance (CR) trait from the ‘CCR13685’ Chinese cabbage (B. rapa subsp. pekinensis) inbred line into an elite pak choi inbred line, ‘GHQ11021’. Genetic analysis of F₂ and BC₁ progeny showed that CR of ‘CCR13685’ was controlled by a single dominant gene. We designed nine candidate sequence‐characterized amplified region markers, K‐1 to K‐9, based on two molecular markers linked to the CR gene. We found that K‐3 co‐segregated with CR and an inoculation test confirmed that K‐3 could be used for MAS. Two introgression lines, BC₃‐1‐4 and BC₃‐2‐18, were developed using K‐3 for foreground selection. These lines displayed the same phenotypic properties as ‘GHQ11021’, but were highly resistant to clubroot, indicating that the CR gene of ‘CCR13685’ had been successfully introduced into pak choi.     

Efficient marker‐assisted backcross conversion of seed‐parent lines to cytoplasmic male sterility

For many crops, cytoplasmic male sterility (CMS) is a cornerstone of hybrid production. Efficient conversion of elite lines to CMS by marker‐assisted backcrossing is therefore desirable. In contrast to gene introgression, for which donor segments around target genes have to be considered, background selection for CMS conversion focuses solely on recovery of the recurrent parent genome. The optimal selection strategies for CMS conversion will consequently differ from those for gene introgression and have not yet been investigated. The objectives of our study were to evaluate and optimize the resource requirements of CMS conversion programmes and to determine the most cost‐effective use of single‐marker (SM) and high‐throughput (HT) assays for this purpose. We conducted computer simulations for CMS conversion of genetic models of sugar beet, rye, sunflower and rapeseed. CMS conversion required fewer resources than gene introgression with respect to population size, marker data points and number of backcross generations. Combining HT assays in early backcross generations with SM assays in advanced backcross generations further increased the cost‐efficiency of CMS conversion for a broad range of cost ratios.     

Evaluation of the Ph‐3 gene‐specific marker developed for marker‐assisted selection of late blight‐resistant tomato

Late blight caused by Phytophthora infestans is one of the most destructive diseases of tomato (Solanum lycopersicum L.) that mainly occurs in cool and wet environments. With the spread of the A2 mating type and new clonal lineages, fewer fungicides provide effective control of the disease, which has increased its worldwide threat. Host resistance could contribute significantly to sustainable disease control. Ph‐3 is a race‐specific late blight resistance gene commonly used in commercial tomato breeding. Availability of precise and easy to use gene‐based markers would facilitate selection. In this study, a Ph‐3 on‐gene cleaved amplified polymorphic sequence (CAPS) marker, Ph3.gsm/HincII, was developed based on the published gene sequence of Ph‐3. The effectiveness of the marker was evaluated along with other published Ph‐3 markers using an F₉ recombinant inbred line (RIL) population derived from NC 23E‐2(93) × L3708. Markers Ph3.gsm/HincII and TG328/BstNI accurately genotyped the RIL population for Ph‐3. In addition, Ph3.gsm/HincII was able to differentiate variable susceptible alleles. This reliable codominant DNA marker would be very useful in marker‐assisted selection, particularly for resistance gene pyramiding.     

Journeys through aroma space: a novel approach towards the selection of aroma‐enriched strawberry cultivars in breeding programmes

Consumers often criticize the sensory quality of modern strawberry cultivars. Therefore, a new and fast workflow for cultivar selection was developed to aid in the development of cultivars with enhanced aroma. This workflow consists of Headspace (HS) solid‐phase microextraction (SPME) fast GC‐MS used for high‐throughput aroma analysis of parents and hybrids. For data analysis, a chemometrical workflow was created. With a principal component analysis (PCA), the aroma similarity between the samples and a target aroma was evaluated. In order to know how the aroma profiles of the parents and hybrids are situated towards this target aroma, the Euclidean distances were calculated. These were then further used for a partial least‐squares (PLS) regression analysis to determine which aroma compounds are responsible for the observed distance to the target. By using this new approach, hybrids showing aroma profiles similar to the target aroma can be identified as most suitable candidates for further breeding cycles. Besides being time‐saving, the suggested workflow introduces aroma analysis as an integral part of breeding programmes. It prevents losing the coherence within the aroma profile and subsequently the loss of important information.     

The multilocular trait of rapeseed is ideal for high‐yield breeding

The multilocular trait is generally considered as a desirable agricultural trait for the high‐yield breeding of Brassica crops and has attracted considerable attention. The siliques of multilocular plants contain more chambers and seeds than those of bilocular rapeseed varieties and, thus, have a higher yield. Furthermore, multilocular plants are precious germplasm resources for the breeding of Brassica crops. In this article, we provide a summary of researches regarding the multilocular trait in rapeseed, including its natural germplasms, silique morphology, genetic models, and regulatory mechanisms. The study will highlight the potential of multilocular rapeseed for high‐yield breeding.     

Marker‐assisted backcross breeding for improvement of drought tolerance in bread wheat (Triticum aestivum L. em Thell)

Drought stress is presently a major productivity limiting factor in wheat. This study developed five wheat lines with inbuilt tolerance to drought stress using marker‐assisted backcross breeding (MABB) approach employing three linked quantitative trait loci (QTLs) in an initial population of 516 BC₁F₁ plants. The high‐yielding wheat cultivar ‘HD2733’ grown over last few years extensively in the eastern plains of India is largely sensitive to drought and is used as the recurrent parent. ‘HI1500’ released for water‐limiting conditions and carrying drought‐tolerant QTLs was used as donor parent. MABB lines were advanced using foreground and background selection, coupled with stringent phenotyping. We identified 29 lines that were homozygous for targeted QTLs in different combinations with background recovery range of 89.2%–95.4%. Further evaluation of selected lines for physiological traits and distinctness, uniformity and stability (DUS) characters under rainfed condition identified five potential varieties for national varietal evaluation programme in the zone. The report is first of its kind in implementing known QTLs for the development of drought‐tolerant wheat lines through MABB approach.     

Maize participatory breeding in Portugal: Comparison of farmer's and breeder's on‐farm selection

“VASO” is a Portuguese participatory maize breeding project (1984), where several maize landraces such as “Pigarro” have been selected both by a farmer's (phenotypic recurrent selection) and a breeder's approach (S2 lines recurrent selection). The objectives of this study were to determine the phenotypic and genotypic responses to participatory selection using these two different approaches, to clarify to which extent both selection methods preserve genetic diversity, and conclude what is the preferred method to apply in sustainable farming systems. The results, obtained via ANOVA, regression analyses and molecular markers, indicate that for both selection methods, genetic diversity was not significantly reduced, even with the most intensive breeder's selection. Although there were some common outputs, such as the determinated versus indeterminated ears, cob and ear weight ratio per ear and rachis 2, specific phenotypic traits evolved in opposite directions between the two selection approaches. Yield increase was only detected during farmer selection, indicating its interest on PPB. Candidate genes were identified for a few of the traits under selection as potential functional markers in participatory plant breeding.     

Identification of recombinants carrying stripe rust resistance gene Yr57 and adult plant stem rust resistance gene Sr2 through marker‐assisted selection

Many stem rust resistance genes have been formally named in wheat. Adult plant stem rust resistance gene Sr2 was mapped in the short‐arm of chromosome 3B. Stripe rust resistance gene Yr57, identified in Aus91463, was mapped about 5 cM away from Sr2 based on its linkage with Sr2‐linked marker gwm533. The objective of this study was to combine Sr2 and Yr57 in a single genotype. A mapping population containing 107 recombinant inbred lines was developed from a cross between Aus91463‐Yr57 and Hartog‐Sr2. This population was tested at the seedling stage in the glasshouse for variation in stripe rust response, and high temperature induced Sr2‐linked seedling chlorosis. The RIL population was screened for Sr2‐linked pseudo black chaff phenotype at the adult plant stage in field. Five recombinants carrying Sr2 and Yr57 in coupling were detected using phenotypic and marker data. Four recombinants also carried leaf rust resistance gene Lr23 from Aus91463. These recombinants are being used as triple rust resistance source in the Australian Cereal Rust Control Program.     

Development of AS‐PCR marker based on a key mutation confirmed by resequencing of Wx‐mp in Milky Princess and its application in japonica soft rice (Oryza sativa L.) breeding

Soft rice with low amylose content (AC) ranging by 5–15% is a unique type with special eating and appearance quality and has become popular in the rice market. We resequenced the Wx‐mp, a key allele from Milky Princess, a Japanese low AC variety, and found that the +473 mutation in exon 4 is the key mutation in both Wx‐mp and its ancestor allele, Wx‐mq from Milky Queen. Based on this functional mutation, an allele‐specific PCR (AS‐PCR) marker was developed and proven in a breeding population derived from a cross between a Chinese late variety Nan Keng 46 (Wx‐mp/Wx‐mp) and an early line Ning 63121(Wx‐b/Wx‐b). Based on the marker‐aided selection by our newly developed AS‐PCR marker for Wx‐mp and the known ST10 marker for Stvb‐i, a total of 12 Wx‐mp homozygotes were selected from 198 F₂ progenies, and four of them were immune to rice stripe virus (RSV) with averagely 11.3 days earlier heading than Nan Keng 46 without significant change in grain yield.