Showing papers in "Plant Breeding in 2019"

Cowpea (Vigna unguiculata): Genetics, genomics and breeding

Abstract: Communicated by: C. Ojiewo Abstract Cowpea, Vigna unguiculata (L.), is an important grain legume grown in the tropics where it constitutes a valuable source of protein in the diets of millions of people. Some abiotic and biotic stresses adversely affect its productivity. A review of the genetics, genomics and breeding of cowpea is presented in this article. Cowpea breeding programmes have studied intensively qualitative and quantitative genetics of the crop to better enhance its improvement. A number of initiatives including Tropical Legumes projects have contributed to the development of cowpea genomic resources. Recent progress in the development of consensus genetic map containing 37,372 SNPs mapped to 3,280 bins will strengthen cowpea trait discovery pipeline. Several informative markers associated with quantitative trait loci (QTL) related to desirable attributes of cowpea were generated. Cowpea genetic improvement activities aim at the development of drought tolerant, phosphorus use efficient, bacterial blight and virus resistant lines through exploiting available genetic resources as well as deployment of modern breeding tools that will enhance genetic gain when grown by sub-Saharan Africa farmers.

Integrated breeding approaches for improving drought and heat adaptation in chickpea ( Cicer arietinum L.)

Abstract: Chickpea (Cicer arietinum L) is a dry season food legume largely grown on residual soil moisture after the rainy season The crop often experiences moisture stress towards end of the crop season (terminal drought) The crop may also face heat stress at the reproductive stage if sowing is delayed The breeding approaches for improving adaptation to these stresses include the development of varieties with early maturity and enhanced abiotic stress tolerance Several varieties with improved drought tolerance have been developed by selecting for grain yield under moisture stress conditions Similarly, selection for pod set in the crop subjected to heat stress during reproductive stage has helped in the development of heat‐tolerant varieties A genomic region, called QTL‐hotspot, controlling several drought tolerance‐related traits has been introgressed into several popular cultivars using marker‐assisted backcrossing (MABC), and introgression lines giving significantly higher yield than the popular cultivars have been identified Multiparent advanced generation intercross (MAGIC) approach has been found promising in enhancing genetic recombination and developing lines with enhanced tolerance to terminal drought and heat stresses

Breeding and genomics status in faba bean (Vicia faba)

Abstract: Faba bean is an important legume crop because of its high‐yield potential and nutrition‐dense grains. There have been significant achievements in faba bean improvement in the last four decades, which led to the doubling of the global yield average. This study reviews the genetic diversity, the breeding methodologies, major achievement on biotic and abiotic traits, and the recent molecular approaches. The high genetic diversity among faba bean accessions has been useful for increasing yield potential of the crop. Substantial increase in yield potential can be gained through the development of cultivars in open pollinated conditions. In the past, many faba bean varieties that are tolerant to abiotic and biotic stresses were released worldwide. The average yield gains varied from 1.65% per year in Syria to 4.17% per year in Ethiopia. The recent advances in molecular technologies will be used to develop more coherent genetic maps, which would also facilitate assembling and ordering genomic scaffolds in a future genome‐sequencing effort and molecular‐breeding approach.

Genomics, genetics and breeding of common bean in Africa: A review of tropical legume project

Abstract: Common bean (Phaseolus vulgaris L.) is an important legume crop worldwide. The International Centre for Tropical Agriculture (CIAT) and its national partners in Africa aim to overcome production constraints of common bean and address the food, nutrition needs and market demands through development of multitrait bean varieties. Breeding is guided by principles of market-driven approaches to develop client-demanded varieties. Germplasm accessions from especially two sister species, P. coccineus and P. acutifolius, have been utilized as sources of resistance to major production constraints and interspecific lines deployed. Elucidation of plant mechanisms governing pest and disease resistance, abiotic stress tolerance and grain nutritional quality guides the selection methods used by the breeders. Molecular markers are used to select for resistance to key diseases and insect pests. Efforts have been made to utilize modern genomic tools to increase scale, efficiency, accuracy and speed of breeding. Through gender-responsive participatory variety selection, market-demanded varieties have been released in several African countries. These new bean varieties are a key component of sustainable food systems in the tropics.

Genetics, genomics and breeding of groundnut ( Arachis hypogaea L.)

Abstract: Groundnut is an important food and oil crop in the semiarid tropics, contributing to household food consumption and cash income. In Asia and Africa, yields are low attributed to various production constraints. This review paper highlights advances in genetics, genomics and breeding to improve the productivity of groundnut. Genetic studies concerning inheritance, genetic variability and heritability, combining ability and trait correlations have provided a better understanding of the crop's genetics to develop appropriate breeding strategies for target traits. Several improved lines and sources of variability have been identified or developed for various economically important traits through conventional breeding. Significant advances have also been made in groundnut genomics including genome sequencing, marker development and genetic and trait mapping. These advances have led to a better understanding of the groundnut genome, discovery of genes/variants for traits of interest and integration of marker-assisted breeding for selected traits. The integration of genomic tools into the breeding process accompanied with increased precision of yield trialing and phenotyping will increase the efficiency and enhance the genetic gain for release of improved groundnut varieties.

Genomics, genetics and breeding of tropical legumes for better livelihoods of smallholder farmers.

Abstract: Legumes are important components of sustainable agricultural production, food, nutrition and income systems of developing countries. In spite of their importance, legume crop production is challenged by a number of biotic (diseases and pests) and abiotic stresses (heat, frost, drought and salinity), edaphic factors (associated with soil nutrient deficits) and policy issues (where less emphasis is put on legumes compared to priority starchy staples). Significant research and development work have been done in the past decade on important grain legumes through collaborative bilateral and multilateral projects as well as the CGIAR Research Program on Grain Legumes (CRP‐GL). Through these initiatives, genomic resources and genomic tools such as draft genome sequence, resequencing data, large‐scale genomewide markers, dense genetic maps, quantitative trait loci (QTLs) and diagnostic markers have been developed for further use in multiple genetic and breeding applications. Also, these mega‐initiatives facilitated release of a number of new varieties and also dissemination of on‐the‐shelf varieties to the farmers. More efforts are needed to enhance genetic gains by reducing the time required in cultivar development through integration of genomics‐assisted breeding approaches and rapid generation advancement.

Marker‐assisted introgression of rare allele of β‐carotene hydroxylase (crtRB1) gene into elite quality protein maize inbred for combining high lysine, tryptophan and provitamin A in maize

Abstract: Vitamin A deficiency in humans is a widespread health problem. Quality protein maize (QPM) is a popular food rich in lysine and tryptophan, but poor in provitamin A (proA). Here, we report the improvement of an elite QPM inbred, HKI1128Q for proA using marker‐assisted introgression of crtRB1‐favourable allele. HKI1128 was one of the parental lines of three popular hybrids in India and was converted to QPM in our earlier programme. Severe segregation distortion for crtRB1 was observed in BC₁F₁, BC₂F₁ and BC₂F₂. Background selection by 100 SSRs revealed mean recovery of 91.07% recurrent parent genome varying from 88.78% to 93.88%. Across years, introgressed progenies possessed higher mean β‐carotene (BC: 9.22 µg/g), β‐cryptoxanthin (BCX: 3.05 µg/g) and provitamin A (proA: 10.75 µg/g) compared to HKI1128Q (BC: 2.26 µg/g, BCX: 2.26 µg/g and proA: 3.38 µg/g). High concentration of essential amino acids, viz. lysine (mean: 0.303%) and tryptophan (0.080%) in endosperm, was also retained. Multi‐year evaluation showed that introgressed progenies possessed similar grain yield (1,759–1,879 kg/ha) with HKI1128Q (1,778 kg/ha). Introgressed progenies with higher lysine, tryptophan and proA hold immense potential as donors and parents in developing biofortified hybrids.

Using yield quantitative trait locus targeted SSR markers to study the relationship between genetic distance and yield heterosis in upland cotton (Gossypium hirsutum)

Abstract: The objective of this study was to examine the relationship between heterosis and genetic distance in upland cotton (Gossypium hirsutum L.). Heterosis in the different environments was evaluated and the relationship between heterosis and genetic distance (GD) was determined based on SSR markers for yield quantitative trait loci (QTL). Yields of seed cotton and lint showed a linear relationship with mid‐parent heterosis (MPH) and better‐parent heterosis (BPH). The variation in heterosis for other traits and their correlation with GD may be due to environmental factors or the effort of QTLs tested in the present study may vary in different environments. The present findings provide a foundation for heterotic grouping of parental lines and breeding of new cotton hybrids with improved seed cotton yield. This study calls for more research with stable QTLs as well as advance molecular marker techniques may be used in predicting yield heterosis in a more precise and reliable manner.

A decade of Tropical Legumes projects: Development and adoption of improved varieties, creation of market-demand to benefit smallholder farmers and empowerment of national programmes in sub-Saharan Africa and South Asia.

Abstract: This article highlights 12 years (2007–2019) of research, achievements, lessons learned, challenges and gaps in discovery‐to‐delivery research in legumes emanating from three projects, collectively called Tropical Legumes (TL) with a total investment of about US$ 67 million funded by the Bill & Melinda Gates Foundation. These projects were implemented by three CGIAR centres (ICRISAT, CIAT and IITA) together with 15 national agricultural research system partners in sub‐Saharan Africa and South Asia. The TL projects together with some of their precursors and complementary projects from other agencies, facilitated the development of 266 improved legume varieties and the production of about 497,901 tons of certified seeds of the target legume crops in the focus countries. The certified seeds have been planted on about 5.0 million ha by more than 25 million smallholder farmers in the 15 countries and beyond, producing about 6.1 million tons of grain worth US$ 3.2 billion. Furthermore, the projects also trained 52 next generation scientists that included 10 women, by supporting 34 Masters degrees and 18 PhD degrees.

Quantitative trait locus analysis for soybean (Glycine max) seed protein and oil concentrations using selected breeding populations

Abstract: Soybean seed protein and oil concentrations are important traits that directly affect the quality of soyfoods. Many studies and breeding programmes have been conducted to find major quantitative trait loci (QTL) that regulate protein and oil concentrations and to develop soybean cultivars with high protein and/or oil content. The purpose of this study was to identify these QTL using a selected breeding population. The population was tested in field conditions over a period of 3 years. Seed protein and oil concentrations were measured each year. Single‐nucleotide polymorphisms (SNPs) were used to construct genetic map using a 180K SoyaSNP array, which identified 1,570 SNPs. We identified 12 QTL for seed protein, 11 for seed oil concentration and four for both traits. Among these, 17 QTL were closely mapped to previously reported QTL, whereas ten sites were novel. Several QTL were detected across at least two experimental years. These loci are good candidate QTL for optimal seed protein and oil concentrations. Our results demonstrate that favourable target QTL can be successfully identified using selected breeding populations.

Genetic dissection of haploid male fertility in maize (Zea mays L.)

Abstract: Haploid genome doubling is a key limiting step of haploid breeding in maize. Spontaneous restoration of haploid male fertility (HMF) provides a method by which costs can be saved and which does not require the use of toxic chemicals, in contrast to the artificial doubling process. To reveal the genetic basis of HMF, haploids were obtained from the offspring of 285 F2:3 families, derived from the cross Zheng58×K22. The F2:3 families were used as female donor and YHI-1 as the male inducer line. The rates of HMF from each family line were evaluated at two field sites over two planting seasons. Quantitative trait loci (QTL) for HMF were identified using a genetic linkage map containing 157 simple sequence repeat (SSR) markers. QTL for HMF displayed incomplete dominance. Transgressive segregation of haploids from F2:3 families was observed relative to haploids derived from the two parents of the mapping population. A total of nine QTL were detected, which were distributed on chromosomes 1, 3, 4, 7, and 8. Three QTL, qHMF3b, qHMF7a, and qHMF7b were detected in both locations, respectively. In our mapping population, HMF was controlled by three major QTL. These QTL could be useful to predict the ability of spontaneous haploid genome doubling in related breeding materials, and to accelerate the haploid breeding process by introgression or aggregation of those QTL.

Origin of early maturing pigeonpea germplasm and its impact on adaptation and cropping systems

Abstract: Pigeonpea breeding activities started about a century ago and for decades only late maturing cultivars dominated the global cultivation. Historically, no early maturing cultivar was available for a very long time and breeding of such varieties started in the third quarter of 20th century but at a low key. From these efforts, some pigeonpea varieties maturing in 90–150 days were bred. Information gathered from various sources revealed that the first few early maturing genotypes originated through spontaneous mutations in the late maturing field‐grown landraces. In other cases, transgressive segregation and induced mutations also produced early maturing varieties. At present, the high yielding early maturing cultivars are contributing significantly towards widening the adaption barriers and in the diversification of some age‐old cropping systems. In this paper, the authors, besides discussing the importance of early maturing cultivars in present agricultural systems, also summarize information related to the origin of primary sources of earliness.

Inheritance of Striga hermonthica adaptive traits in an early‐maturing white maize inbred line containing resistance genes from Zea diploperennis

Abstract: Striga hermonthica parasitism is a limiting factor to cultivation of maize in the savannas of sub‐Saharan Africa (SSA) which constitutes the maize belt of the subregion. About 75% of the land cultivated to maize in agro‐ecological zones in SSA is endemic to S. hermonthica. Maize yield losses under severe Striga infestation could be as high as 100% (Kroschel, 1999; Lagoke, 1998) especially when infestation coincides with the vegetative stage of growth in maize, during the growing season. Farmers of West and Central Africa (WCA) are most often compelled to abandon their farms under heavy Striga infesta‐ tion. Several chemical and cultural methods have been used for Striga control but have proved ineffective and unsustainable for the farm‐ ers in the Striga endemic zones of the subregion. Striga resistance Received: 15 October 2018 | Revised: 11 March 2019 | Accepted: 16 March 2019 DOI: 10.1111/pbr.12707

Density enhancement of a faba bean genetic linkage map (Vicia faba) based on simple sequence repeats markers

Abstract: Genetic mapping for faba bean lags far behind other major crops. Density enhancement of the faba bean genetic linkage map was carried out by screening 5,325 genomic SSR primers and 2033 expressed sequence tag (EST)‐SSR primers on the parental cultivars '91825' and 'K1563'. Two hundred and fifteen genomic SSR and 133 EST‐SSR primer pairs that detected polymorphisms in the parents were used to screen 129 F₂ individuals. This study added 337 more SSR markers and extended the previous linkage map by 2928.45 cM to a total of 4516.75 cM. The number of SSR markers in the linkage groups varied from 12 to 136 while the length of each linkage group ranged from 129.35 to 1180.21 cM. The average distance between adjacent loci in the enhanced genetic linkage map was 9.71 cM, which is 2.79 cM shorter than the first linkage map of faba bean. The density‐enhanced genetic map of faba bean will be useful for marker‐assisted selection and breeding in this important legume crop.

Pigeonpea improvement: An amalgam of breeding and genomic research

Abstract: In the past five decades, constant research has been directed towards yield improvement in pigeonpea resulting in the deployment of several commercially acceptable cultivars in India. Though, the genesis of hybrid technology, the biggest breakthrough, enigma of stagnant productivity still remains unsolved. To sort this productivity disparity, genomic research along with conventional breeding was successfully initiated at ICRISAT. It endowed ample genomic resource providing insight in the pigeonpea genome combating production constraints in a precise and speedy manner. The availability of the draft genome sequence with a large‐scale marker resource, oriented the research towards trait mapping for flowering time, determinacy, fertility restoration, yield attributing traits and photo‐insensitivity. Defined core and mini‐core collection, still eased the pigeonpea breeding being accessible for existing genetic diversity and developing stress resistance. Modern genomic tools like next‐generation sequencing, genome‐wide selection helping in the appraisal of selection efficiency is leading towards next‐generation breeding, an awaited milestone in pigeonpea genetic enhancement. This paper emphasizes the ongoing genetic improvement in pigeonpea with an amalgam of conventional breeding as well as genomic research.

Market‐led options to scale up legume seeds in developing countries: Experiences from the Tropical Legumes Project

Abstract: There are several hurdles to ensure sustainable seed production and consistent flow of improved legume varieties in sub‐Saharan Africa (SSA) and South Asia (SA). The unreliable demand, autogamous nature of most of the grain legumes, and slow variety replacement rate by smallholder farmers do not provide strong incentive for private seed companies to invest in legume seed business. Unless a well thought‐out and comprehensive approach to legume seed delivery is developed, current seed shortages will continue, eroding emerging market opportunities. The experiences reported here are collated through a 10‐year partnership project, the Tropical Legumes in SSA and SA. It fostered innovative public–private partnerships in joint testing of innovative market‐led seed systems, skills and knowledge enhancement, de‐risking private sector initiatives that introduced in new approaches and previously overlooked entities in technology delivery. As new public and private seed companies, individual seed entrepreneurs and farmer organizations emerged, the existing ones enhanced their capacities. This resulted in significant rise in production, availability and accessibility of various seed grades of newly improved and farmer demanded legume varieties in the target countries.

Public sector soybean (Glycine max) breeding: Advances in cultivar development in the African tropics

Abstract: Formal public sector soybean breeding in Africa spans over four decades, and it was initiated by the International Institute of Tropical Agricultural (IITA). As the demand of soybean continues to outstrip production, strategic projects such the Tropical Legume (TL) were initiated, in which the main goal was to enhance the productivity of soybean in the farmers’ fields in Sub-Saharan Africa. One of the strategies to enhance the productivity of soybean in the farmers’ fields is through developing and deploying improved soybean varieties in the target countries. Through the TL I and TL II projects, a number of varieties were released in the target countries, Kenya, Nigeria, Malawi and Mozambique by employing participatory variety selection (PVS). This review provides highlights of the achievements made by IITA breeding programme and insights of what needs to be done to enhance yield improvement for soybean in Africa using demand-driven breeding approaches.